title: 3T3_t6d_rep2_pro

city: Farmington

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

description: nascent RNA

data_processing:
Library strategy: PRO-seq
adapter trimming: cutadapt 1.8.1
FASTQ deduplication: https://raw.githubusercontent.com/WarrenDavidAnderson/genomeAnalysis/master/PROseq/deduplicator.py
FASTX trimming and reverse complementing: fastx_trimmer, fastx_reverse_complement 0.0.14. Note that the first 8 bases of the read are a UMI and need to be trimmed.
alignment: bowtie2 2.2.5
file manipulation: samtools 1.2
file manipulation: seqOutBias v1.1.3
all PRO-seq details and code: https://github.com/WarrenDavidAnderson/genomeAnalysis/tree/master/PROseq
all ATAC-seq details and code: https://github.com/WarrenDavidAnderson/genomeAnalysis/tree/master/ATACseq
Genome_build: mm10
Supplementary_files_format_and_content: PRO: stranded bigWig counts files; ATAC: bigWig counts file

source_name: 3T3-L1 cells

growth_protocol: 3T3-L1 cells are from Dr. Thurl Harris and were were grown in high glucose Dulbecco’s Modified Eagle Medium containing 10% newborn calf serum, 1% fetal calf serum, 100 U/mL penicillin g-sodium, and 100 μg/mL streptomycin sulfate

treatment_protocol: A final concentration of 0.25 U/mL Insulin, 250 nM dexamethasone, and 0.5 mM 3-isobutyl-1-methylxanthine was added at indicated times

tag: cell line

value: 3T3-L1 cells

tag: treatment

value: 6 days adipogenesis cocktail


title: 3T3_t6d_rep3_pro

status: Public on May 13 2020

type: SRA

first: Michael

country: USA

description: nascent RNA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus


title: MacTRAP_ub2

city: Marburg

first: Andreas

last: Hofmeister

state: Hessen

address: Baldingerstrasse 1

department: Zentrum für Innere Medizin

country: Germany

institute: Philipps-Universität Marburg

data_processing:
Basecalling was performed with RTA 1.18.64. Bcl conversion into Fastq were performed using bcl2fastq version 2.19.0.316. Illumina Sequencing kit V4 and Illumina HCS 2.2.58 Sequencing software was used for RNA-Seq.
The RNA-Seq. data were mapped against the mouse reference genome GRCm38 using Hisat2. The obtained SAM files were converted to BAM files using SAMtools "sort" command and subsequently made compatible for usage of the ".gtf" file of ENSEMBL (ftp://ftp.ensembl.org/pub/release-89/gff3/mus_musculus/). The resulting files were analyzed with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: .txt

molecule: polyA RNA

source_name: kidney macrophages

extract_protocol:
Grgic protocol: TRAP, modified (Based on published protocol: M Heiman, Cell 2008, 135 (4):738-48.)
RNA libraries were prepared at DKFZ Heidelberg according to SmarTer ultra low input protocol for RNA-sequencing using Illumina HiSeq2000 platform.

tag: strain

tag: age

value: 9 weeks

tag: immunopreciptate

value: unbound


title: lckgfp_s120

city: Chicago

first: Elizabeth

last: Jerison

state: IL

address: 529 E 57th St

department: Physics

institute: University of Chicago

data_processing:
STAR (2.5)
Htseq (0.8.0) htseq-count -m intersection-nonempty --nonunique all
Genome_build: GRCz10
Supplementary_files_format_and_content: Raw counts of numbers of reads aligned to each feature for each cell, in tab-separated format (lckgfp_counts.txt)

organism: Danio rerio

source_name: Danio rerio tail

extract_protocol:
Lysis was performed as described in Schaum et al., Nature 2018
A Smart-Seq2 based protocol was used for reverse transcription and cDNA amplification, and a Nextera based protocol was used for library preparation, as described in Schaum et al., Nature 2018

treatment_protocol: Liberase TL (100 ug/mL) and manual trituration was used to dissociate tail tissue. Cells were FACS sorted (FITC+)

tag: line

tag: tissue

value: tail

tag: devlopmental stage

value: 15 dpf


title: lckgfp_s115


title: 70

city: Cambridge

first: Kathleen

middle: Marie

last: Smith

state: MA

address: 200 Sidney Street

department: Systems Computational Biology

institute: AbbVie

description:
Untreated_Les
processed data file: TPM93.Bissonnette.csv

data_processing:
FastQC was applied on raw fastq files to examine the sequence quality.
Kallsito
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: TPM93.Bissonnette.csv: Comma-separated text file includes TPM values.

organism: Homo sapiens

source_name: Skin biopsy

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit.
RNA was depleted of ribosomal RNA using the Ribo-Zero method (Illumina) and libraries prepared.

tag: subject id

tag: cohort

value: Skin

tag: response

tag: batch


title: 3T3_t6d_rep1_pro

description: nascent RNA


title: lckgfp_s114


title: MacTRAP_ub1


title: 3T3_t60min_rep3_pro

description: nascent RNA

value: 60 minutes adipogenesis cocktail


title: 69

description:
NonLes
processed data file: TPM93.Bissonnette.csv


title: MacTRAP_b2

value: bound


title: lckgfp_s113


title: 72


title: 3T3_t60min_rep1_pro

description: nascent RNA


title: 67


title: 3T3_t60min_rep2_pro

description: nascent RNA


title: PDX60

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

country: Spain

institute: Institut Catala d'Oncologia IDIBELL

data_processing:
Illumina Casava1.7 software used for basecalling.
The RNA sequencing reads were trimmed for adaptors, masked for low-complexity or low-quality sequence, and subsequently mapped to the human genome (hg19) using STAR (version 2.4.0f1)
The SAM/BAM files were further processed using the SAMtools (version 0.1.18) and read count quantitations were obtained using BEDTools multicov (version 2.25.0).
Gene expression was quantified by as transcripts per million (TPM).
Genome_build: hg19
Supplementary_files_format_and_content: log2 TPM data matrix of gene expression.

source_name: PDX

growth_protocol: Human cancer tissue samples from surgery or biopsy were implanted into the mammary fat pad of 6‐week‐old female athymic HsdCpb:NMRI‐Foxn1nu or NOD mice. The PDX were established for at least 3 passages.

extract_protocol:
Total RNA from tumor tissue lines was extracted using the RNeasy kit (Qiagen) and RNA quality was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols

treatment_protocol: Basal conditions.

tag: tissue type

value: Mammary fat pad of nudeMouse

tag: disease state

value: Human breast cancer


title: PDX341


title: lckgfp_s112


title: 66


title: PDX296


title: lckgfp_s111


title: 65


title: 3T3_t4h_rep2_pro

description: nascent RNA

value: 4 hours adipogenesis cocktail


title: 64


title: lckgfp_s110


title: PDX280


title: 63


title: lckgfp_s109


title: PDX270


title: PDX236


title: 3T3_t40min_rep2_pro

description: nascent RNA

value: 40 minutes adipogenesis cocktail


title: 62


title: lckgfp_s108


title: 3T3_t40min_rep3_pro

description: nascent RNA


title: lckgfp_s107


title: PDX196


title: PDX179


title: 3T3_t4h_rep3_pro

description: nascent RNA


title: lckgfp_s106


title: 3T3_t40min_rep1_pro

description: nascent RNA


title: 61


title: 43

value: Responder


title: PDX288


title: 38

description:
UST_Les
processed data file: TPM93.Bissonnette.csv


title: lckgfp_s105


title: 3T3_t3h_rep3_pro

description: nascent RNA

value: 3 hours adipogenesis cocktail


title: lckgfp_s104


title: PDX339


title: 37


title: 3T3_t4h_rep1_pro

description: nascent RNA


title: 3T3_t3h_rep2_pro

description: nascent RNA


title: PDX332


title: 3T3_t3h_rep1_pro

description: nascent RNA


title: 3T3_t2h_rep3_pro

description: nascent RNA

value: 2 hours adipogenesis cocktail


title: lckgfp_s103


title: 34


title: lckgfp_s102


title: PDX302OR


title: 3T3_t2h_rep2_pro

description: nascent RNA


title: PDX302


title: lckgfp_s101


title: 32


title: 3T3_t2h_rep1_pro

description: nascent RNA


title: 31


title: lckgfp_s099


title: lckgfp_s100


title: 30


title: PDX230OR1


title: PDX230


title: 3T3_t20min_rep2_pro

description: nascent RNA

value: 20 minutes adipogenesis cocktail


title: PDX98


title: 29


title: 3T3_t20min_rep1_pro

description: nascent RNA

value: 3T3-L1 cells


title: 3T3_t0_rep3_pro

description: nascent RNA


title: 3T3_t20min_rep3_pro

description: nascent RNA


title: lckgfp_s096


title: 28


title: 27


title: lckgfp_s095


title: PDX197


title: 33


title: 3T3_t0_rep2_pro

description: nascent RNA


title: PDX44


title: PDX291B


title: 26


title: 25


title: lckgfp_s094


title: PDX127


title: 3T3_t0_rep1_pro

description: nascent RNA


title: PDX137


title: Standard, C57BL/6 Mouse Genomic DNA

city: Buffalo

first: Jian

last: Feng

state: NY

address: 955 Main Street, Room 3102

department: Department of Physiology and Biophysics

institute: State University of New York at Buffalo

description:
2 replicates
PCR Amplicon

library_source: genomic

data_processing:
Library strategy: Amplicon sequencing
Per-cycle basecall (BCL) were converted to per-read FASTQ files using bcl2fastq version 2.20.0.422 using default parameters.
Forward and reverse barcode attachment sites were trimmed using cutadapt version 1.16.
Forward and reverse read-pairs were merged using vsearch fastq_mergepairs and the merged reads with greater than one expected error were filter out.
Merged reads were then classified as either human or mouse using vsearch –usearch_global with the percent identity cutoff set at 99%.
The reference sequence used for human 18S was AGCTAATACATGCCGACGGGCGCTGACCCCCTTCGCGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTCAGCCCCTCTCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCTTTGGTGACTCTAGA and the reference sequence used for mouse 18S was AGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATCAAAACCAACCCGGTGAGCTCCCTCCCGGCTCCGGCCGGGGGTCGGGCGCCGGCGGCTTGGTGACTCTAGA.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: An Excel file containing the number of reads mapped to human 18S or mouse 18S in each sample.

molecule: genomic DNA

source_name: From C57BL/6J mouse

growth_protocol: Naïve hPSCs were maintained on mitomycin C-treated mouse embryonic fibroblast (MEF) feeders (5-6 × 104/cm2) in 2iLI medium (50% glucose-free DMEM/F12 and 50% glucose-free Neurobasal, 5 mM glucose, 1 mM glutamine, 1% NEAA, 0.1 mM β-mercaptoethanol, 100 U/ml penicillin, 100 ug/ml streptomycin, 5 mg/mL bovine serum albumin to maintain osmolarity, 20 ng/mL recombinant human LIF, 18 µg/ml human insulin, 1 μM PD0325901, and 3 μM CHIR99021). Naïve hPSCs were passaged every 3 days with TrypLE. All naïve hPSCs were cultured in 5% O2 and 5% CO2.

extract_protocol:
Mouse embryos or human cells were homogenized in proteinase K solution (100 mM Tris-HCl pH8.0, 5 mM EDTA, 0.2% SDS, 200 mM NaCl, 250µg/ml Proteinase K) and incubated in the same solution at 55°C for 12-18 hours. Pheno/chloroform extraction was then used to extract genomic DNA.  The V3 regions of both human and mouse 18S ribosome genes were amplified from standard  samples or genomic DNA extracted from chimera using human/mouse universal primers containing barcode attachment sites on the 5’ ends (Forward: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGAGCTAATACATGCCGACGGG; Reverse: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTCTAGAGTCACCAAAGCCGC; barcode attachment sites were underlined) and Hotstar plus kit (Qiagen) with an optimized PCR protocol (95°C, 5min; 94°C, 30s; 58°C, 30s; 72°C, 1min; 40 cycles; 72°C, 10min). PCR product from each sample was gel-extracted and purified with QIAquick Gel Extraction Kit (Qiagen)
Purified PCR products were barcoded and library prepared using PE150 kit (illumina)

treatment_protocol: Naive human PSCs were dissociated to single cells with TrypLE for 5-6 minutes and placed on 10 cm dishes for 45 minutes to remove MEF cells through attachment. The supernatant, which contained the hPSCs, was removed from the dish and centrifuged for 10 min at 2000 rpm. Cells in the pellet were resuspended in Mouse Blastocysts Injection Buffer (HEPES-buffered DMEM with 5% FBS). 10-12 naive hPSCs were injected to a C57BL/6J mouse blastocyst, which was obtained by superovulation from 3-4 week old C57BL/6J female mice. Injected blastocysts were transferred bilaterally to uterus of pseudopregnant CD-1 female mice at 7-9 weeks of age, with 14-18 blastocysts transferred per mouse. At Day 17.5, mouse embryos were retrieved and half of each mouse embryo cut sagittally were used in DNA extraction.

tag: sample type

value: Standard Sample


title: lckgfp_s098


title: lckgfp_s093


title: 24


title: 3a_KO_25_Liver_RNA

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

data_processing:
Libraries were sequenced on the HiSeq2500 (2 X 101 bp or 2×100 bp paired-end reads, illumina) or Nextseq500 (75 bp or 86bp, single read, illumina)
Low quality bases and adapters in sequenced reads were trimmed with cutadapt-1.9.1
For WGBS analysis, the trimmed reads were mapped to the mouse genome (mm10) by Bismark software-v0.15.0 with bowtie2 (version 2.2.8) and default settings, and the mapped reads with high mapping quality (MAPQ>=20) were used for extraction of methylated cytosines by the Bismark methylation extractor with --ignore 10 --ignore_3prime 5 options (single-end reads) or with --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5 options (paired-end reads).
For allelic methylation analysis, the trimmed reads were mapped to both B6 mouse genome (mm10) and MSM/ms mouse genome independently by Bismark software-v0.15.0 with bowtie2 (version 2.2.8) and default settings, and the reads mapped to the same chromosome and positions of both B6 and MSM/ms genomes with high mapping quality (MAPQ>=20) were used for further analysis. MSM/ms mouse genome were reconstructed from mm10 using the SNPs (NIG Mouse Genome Database (MSMv4HQ, http://molossinus.lab.nig.ac.jp/msmdb/index.jsp)). Chromosomes Y and M were ommited from MSM/ms genomes because of lack of the SNPs information.
For caluculation of allelic methylation levels, the B6-derived and MSM/ms-derived sequenced reads were selected based on the MSM/ms SNPs data which were not in CpG sites and the patterns of bisulfite conversion. Methylated cytosines were extracted from the reads by the Bismark methylation extractor with --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5 options. For allelic methylation analysis with methyl-seq libraries, only the original bottom (OB) data were used for analysis of methylation status and methylation percentages were represented at the sites which have equal or more than 5 read depth.
For RNA-seq analysis, the sequenced reads were mapped to the mouse reference genome (mm10) using tophat-2.1.0 11 with the GENCODE version M9 annotation gtf file and the aligner Bowtie2-2.2.5 6 after trimming adaptor sequences and low-quality bases by cutadapt-1.9.1 12. For allelic expression analysis of RNA-seq, the trimmed reads were also mapped to MSM genomes described as above, and the reads mapped to the same chromosome and positions of both B6 and MSM/Ms genomes with high mapping quality (MAPQ>=20) were used for further analyses. The expression level of each gene was calculated as reads per kilobase per million mapped reads (RPKM) by cufflinks-2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bedGraph colums: <chromosome> <start position> <end position> <methylation percentage>, *The coordinates are zero-based, half-open.
Supplementary_files_format_and_content: ProcessedDataMatrixRPKM.txt:Tab-delimited text file includes RPKMs for each sample.

growth_protocol: MEFs were isolated from E14.5 embryos and were cultured in DMEM (Nacalai tesque) with 2 mM L-glutamine (Nacalai tesque), 100× nonessential amino acids (NEAA) (Nacalai tesque), 100 U/ml penicillin, 100 mg/ml streptomycin (P/S) (Nacalai tesque) and 10% Fetal Bovine Serum (FBS) (GIBCO).

extract_protocol:
PureLink Genomic DNA mini kit (invitrogen) for genomic DNA and RNAeasy plus Mini Kit (QIAGEN) or NucleoSpin RNA plus (MACHEREY-NAGEL) for RNA.
For methyl-seq library preparation, 3μg of genomic DNA was sheared by covaris. Libraries were constructed using SureSelectXT Mouse Methyl-Seq Reagent Kit (Agilent Technologies). Bisulfite treatment was perfomed by EZ DNA methylation-GOLD kit (ZYMO RESEARCH). For whole genome bisulfite sequencing library, 500ng of DNA was sheared by covaris and ligated with methylated adapters supplied by TruSeqTM DNA, Sample Prep Kit-v2 (Illumina). Subsequently, DNA was bisulfite-treated using EZ DNA Methylation-Gold KitTM according to the supplier’s instruction. Final library amplification was performed using Pfu Turbo Cx (Agilent Technologies). The libraries were then sequenced on HiSeq 2500 (2 X 101 bp paired-end reads, Illumina). To generate RNA-seq libraries, Truseq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier’s instruction.

value: Liver

tag: passage

tag: gender

value: Male

tag: analysis method

value: RNAseq


title: lckgfp_s092

value: tail

value: 15 dpf


title: PDX102


title: 3a_KO_25_Heart_RNA

value: Heart


title: lckgfp_s097


title: 23

value: Skin


title: PDX156

value: Mammary fat pad of nudeMouse


title: lckgfp_s091


title: WT_4_Heart_RNA


title: lckgfp_s089


title: PDX124

value: Human breast cancer


title: WT_4_Liver_RNA


title: 21


title: 3b_KO_MEFs_RNA

source_name: 3b KO_2i-MEFs_RNAseq

value: MEFs

value: F1 (129X1/SvJ and MSM/Ms)

value: Female


title: 22

value: Responder


title: lckgfp_s090


title: 20

description:
ADA_Les
processed data file: TPM93.Bissonnette.csv


title: lckgfp_s088


title: 18


title: 3a_KO_MEFs_RNA

source_name: 3a KO_2i-MEFs_RNAseq


title: PDX93


title: lckgfp_s087


title: 17


title: lckgfp_s086


title: PDX93OR6


title: 3a_KO_MEFs_GSK_RNA


title: 16


title: 3a_KO_MEFs_DMSO_RNA


title: lckgfp_s085


title: 15


title: WT_MEFs_GSK_RNA


title: lckgfp_s084


title: CONTROL 1

city: Montreal

first: Cal

last: Liao

state: QC

address: 1033 Avenues des Pins

country: Canada

institute: Mcgill University

data_processing:
Pseudo-alignment was done with salmon with 200 bootstraps and default settings
Genome_build: Ensembl 94
Supplementary_files_format_and_content: Salmon folder output

source_name: DAOY cells

growth_protocol: Passaged every 2-3 days at 80% confluence

extract_protocol:
RNA extraction was done using RNAeasy kit and the standard protocol for this
Library construction was done using the TruSeq library kit following the standard protocol

tag: cell line

tag: genotype/variation

value: control


title: WT_MEFs_DMSO_RNA

tag: strain


title: 14


title: OVEREXPRESSED 3

value: overexpressed


title: 13


title: OVEREXPRESSED 2


title: lckgfp_s082


title: iPSCNK

city: La Jolla

first: Benjamin

last: Goldenson

state: CA

address: 2880 Torrey Pines Scenic Dr

institute: UCSD

data_processing:
Raw image data file from high-throughput sequencing (illumina) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base calling)
Raw sequencing reads were filted as follow: (1) Remove reads containing adaptors;  (2) Remove reads containing N > 10% (N represents base that could not be determined);  (3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
Clean reads were mapped to human genome using STAR software. In order to avoid losing a lot of effective junction reads,  we use STAR software to alignment for RNA-seq sequencing data analysis, the junction reads can be positioned precisely. Reads were mapped to exon, intron and intergenic.
Gene expression level was estimated by the abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to be proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments.(Mortazavi et al. 2008).
Genome_build: Homo_sapiens_hg38
Supplementary_files_format_and_content: tab-delimited file includes FPKM values for all the samples

source_name: NK cells derived from iPSC

growth_protocol: NK cells were harvested after they reached maturity and co-cultured with irradiated K562-mbIL-21-4-1BB artificial antigen presenting cells (aAPCs) for expansion with media containing RPMI 1640 and 10% FBS; supplemented with 50 units/mL of hIL-2 (Peprotech).

extract_protocol:
Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ubilical cord blood

tag: cell type

value: NK cells derived from iPSC

tag: expansion method

value: using K562-41BB-mbIL21


title: lckgfp_s083

tag: line

tag: tissue


title: lckgfp_s081

tag: devlopmental stage


title: OVEREXPRESSED 1


title: UCBNK56 Post APC donor 4

tag: individual

value: donor 4

tag: treatment

value: UCB56 NK cells isolated from the UCB unit

tag: time

value: Post APC


title: 10

tag: subject id

tag: cohort

tag: response

tag: batch


title: PDX94

tag: tissue type

tag: disease state


title: 9


title: CONTROL 3

tag: passage

tag: cell line


title: CONTROL 2

tag: genotype/variation


title: UCBNK34 Pre APC donor 4

source_name: NK cells derived from CD34+ cells isolated from ubilical cord blood

tag: cell type

value: UCB34 NK cells differentiated from CD34+ cells

value: Pre APC


title: lckgfp_s079

value: tail

value: 15 dpf


title: UCBNK56 Pre APC donor 3

value: donor 3

value: NK cells derived from CD34+ cells isolated from ubilical cord blood

tag: expansion method


title: 8

value: Skin


title: UCBNK34 Post APC donor 4


title: lckgfp_s078

tag: line


title: 7

tag: tissue


title: UCBNK56 Post APC donor 3


title: lckgfp_s077

tag: devlopmental stage


title: 11


title: 6


title: MV_Ctrl_DMSO_3_RNAseq

city: Helsinki

first: Olli

last: Dufva

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description: RNA sequencing of cells expressing indicated sgRNAs after 72 h treatment with decitabine (100 nM) and/or recombinant human interferon gamma (100 ng/ml) or DMSO.

data_processing:
Basecalls performed using standard Illumina base-caller
RNA-seq reads were pre-processed using Trimmomatics v0.32 with the following configurations ILLUMINACLIP:TruSeqAdapters-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Pre-processed RNA-seq reads were aligned to the hg38 genome assembly (EnsEMBL v82) using the STAR per-sample 2-pass mapping strategy. STAR v2.3.0e aligner was used with the following configurations --outSAMattributes All --outSAMunmapped Within. The STAR indexes were built from primary assembly sequences and by taking into account transcript annotations.
PCR duplicates were marked with the MarkDuplicates tool of PICARD v1.63 with the following configurations CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT
Counts were calculated using subreadR as implemented in the statistical environment R (v.3.3.0).
Genome_build: hg38 genome assembly, EnsEMBL v82
Supplementary_files_format_and_content: Tab-delimited text file (.txt). Columns: 1) EnsEMBL gene id, 2) gene model's start coordinate, 3) gene model's stop coordinate, 4) gene model's chromosome, 5) gene name, 6) biotype information, 7) raw count value

source_name: MOLM13 cell line

growth_protocol: Cells were cultured in RPMI-1640 (Lonza) with 10% FBS, 2 mM L-glutamine, 100 U/mL penicillin, and 100 µg/mL streptomycin.

extract_protocol:
RNA was extracted using miRNeasy Mini Kit (Qiagen). The following QC and library construction steps wer performed at Novogene using the lncRNA-seq pipeline. Nanodrop was used for a preliminary quantitation of the RNA concentration. Then agarose gel electrophoresis was performed to test the RNA degradation and potential contamination and Agilent 2100 was used to test the RNA integrity and concentration quantification.
rRNA was removed using the Ribo-Zero kit. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs (dUTP, dATP, dGTP, and dCTP), RNase H and DNA polymerase I were added to initiate the second-strand synthesis, followed by purification by AMPure XP beads, terminal repair, polyadenylation, sequencing adapter ligation, size selection, and degradation of second-strand U-contained cDNA by the USER enzyme. The strand-specific cDNA library was generated after the final PCR enrichment. The library quality control consisted of three steps: (1) Qubit 2.0: tests the library concentration preliminarily, (2) Agilent 2100: tests the insert size, (3) Q-PCR: quantifies the library effective concentration precisely. The qualified libraries were then fed into Illumina sequencers (Illumina Novaseq 6000) after pooling according to their effective concentration and expected data volume with paired end 150 bp sequencing strategy.

treatment_protocol: Cells were plated on 6-well plates at 1.5 million cells/well in a volume of 3 ml and treated with 100 nM decitabine (Selleck) or DMSO as a control, both in the presence or absence of 100 ng/ml recombinant human interferon gamma (Peprotech). After 3 days, the cultures were washed with PBS and 50% of the cells were harvested for RNA extraction.

tag: cancer type

value: acute myeloid leukemia

tag: sgrna

value: Control

value: DMSO

tag: replicate


title: MV_Ctrl_IFN_1_RNAseq

tag: treatment

value: IFNy


title: MV_Ctrl_IFN_2_RNAseq


title: 4

tag: subject id

tag: cohort

value: Responder


title: MV_Ctrl_IFN_3_RNAseq


title: MV_Ctrl_DMSO_2_RNAseq


title: lckgfp_s080


title: UCBNK34 Pre APC donor 3

tag: individual

value: ubilical cord blood

tag: time


title: MV_Ctrl_DMSO_1_RNAseq


title: UCBNK34 Post APC donor 3

value: using K562-41BB-mbIL21


title: 3

tag: response

tag: batch


title: MV_Ctrl_DCIFN_3_RNAseq

tag: cell line


title: lckgfp_s075


title: 2


title: UCBNK56 Pre APC donor 2

value: donor 2

tag: passage


title: UCBNK56 Post APC donor 2

tag: cell type

value: UCB56 NK cells isolated from the UCB unit


title: 1


title: lckgfp_s074


title: lckgfp_s073


title: lckgfp_s072


title: UCBNK34 Pre APC donor 2

tag: expansion method


title: MV_Ctrl_DCIFN_2_RNAseq


title: MV_Ctrl_DCIFN_1_RNAseq


title: UCBNK34 Post APC donor 2

value: Post APC


title: ampicillin/vancomycin-treated mice 1 day-post-infection (dpi) Chikungunya virus

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v3.0.2)
sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v3.0.2)
barcode processing, Cell Ranger Single Cell Software Suite (v3.0.2)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v3.0.2)
alignment, Cell Ranger Single Cell Software Suite (v3.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

source_name: leukocytes of the peripheral blood

extract_protocol:
Peripheral blood leukocytes were collected from AV or vehicle-treated mice (uninfected or 1 dpi) from three biological replicates per group and pooled. Leukocytes were subjected to CD4/CD8/CD19 depletion. Leukocytes of the peripheral blood were isolated following two rounds of ACK lysis. T and B cells were depleted using CD4, CD8, and CD19 microbeads (Millitenyi) to enrich for myeloid cells of the peripheral blood. Cells were resuspended at 100 cells/μL in PBS containing 0.04% (w/v) BSA to minimize cell loss and aggregation. ∼17,500 cells were partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) to achieve single cell resolution for a maximum of 10,000 individual cells per sample.
For gene expression libraries (GEX), Isolated single cell suspensions were subjected to droplet-based massively parallel single-cell RNA sequencing using Chromium Single Cell 3’ v2 Reagent Kit in a BSL-3 level laboratory as per manufacturer’s instructions (10x Genomics). Briefly, cell suspensions were loaded at 1,000 cells/uL with the aim to capture 10,000 cells/well. The 10x Chromium Controller generated GEM droplets, where each cell was labeled with a specific barcode, and each transcript labeled with a unique molecular identifier (UMI) during reverse transcription. The barcoded cDNA was isolated via a Dynabeads MyOne SILANE bead cleanup mixture and amplified 8 cycles. Amplified cDNA was purified via SPRI bead cleanup and removed from the BSL-3 space for library generation.  Amplified cDNA underwent fragmentation, end repair, A-tailing, adapter ligation and sample index PCR as per the manufacturer’s instructions to generate gene expression libraries. Libraries were sequenced on a NovaSeq S2 (200 cycle) flow cell, targeting 50,000 read pairs/cell.

tag: strain

tag: mouse genotype

value: wt

value: leukocytes of the peripheral blood

value: ampicillin/vancomycin

tag: infection


title: lckgfp_s071

tag: line

tag: tissue

value: tail

tag: devlopmental stage

value: 15 dpf


title: MV_Ctrl_DC_3_RNAseq

tag: cancer type

tag: sgrna

tag: treatment

value: Decitabine

tag: replicate


title: T1 replicate 3

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and  employed a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using STAR2 and counted for gene associations against the UCSC genes database with HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.

source_name: cell line

extract_protocol:
RNA was extracted from cell cultures every two weeks during the exponential growth phase; RNA was isolated from 0.5-1.0×106 cells. Total RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: transfection

value: NTRK2 inserts of TrkB.T1


title: lckgfp_s076


title: lckgfp_s070


title: MV_Ctrl_DC_2_RNAseq

value: acute myeloid leukemia


title: ampicillin/vancomycin-treated naïve mice (0 dpi)


title: Vehicle-treated mice 1 day-post-infection (dpi) Chikungunya virus

value: vehicle


title: lckgfp_s069


title: Vehicle-treated naïve mice (0 dpi)


title: T1 replicate 2

value: NTRK2 inserts of TrkB.T2


title: lckgfp_s068


title: T1 replicate 1


title: lckgfp_s067


title: GFP replicate 2

value: NTRK2 inserts of GFP


title: MV_CIITA_IFN_3_RNAseq

value: CIITA

value: IFNy


title: MV_Ctrl_DC_1_RNAseq

value: Control


title: MV_CIITA_IFN_2_RNAseq


title: GFP replicate 1


title: MV_CIITA_DMSO_2_RNAseq

value: DMSO


title: FL replicate3

value: NTRK2 inserts of TrkB.FL


title: lckgfp_s064


title: MV_CIITA_DMSO_3_RNAseq


title: lckgfp_s066


title: FL replicate2


title: GFP replicate 3


title: lckgfp_s065


title: MV_CIITA_IFN_1_RNAseq


title: FL replicate1


title: lckgfp_s062


title: MV_CIITA_DCIFN_3_RNAseq


title: MV_CIITA_DCIFN_2_RNAseq


title: Repeat3_Serum_Starved_Day9

city: Bethesda

first: Katherine

middle: MacLean

last: Peterson

state: MD

address: Building 6 Room 107B

institute: NEI, NIH

data_processing:
Alignment of the sequence files was performed using Novoalign (v. 3.02.00) against the UCSF hg19 refFlat.  Counts were determined using HTseq (v. 0.61) using the mode intersection-strict.  DESeq (v. 1.12.1) with the default settings on R(v. 3.0.1) was used to identify differentially expressed genes (14, 15).  DESeq uses a negative binomial statistical model for its analysis.
Genome_build: Hg19
Supplementary_files_format_and_content: Counts from Htseq with rows of genes and columns of samples

source_name: ARPE19 retinal pigment epithelial cells

growth_protocol: ARPE19 cells were cultured in DMEM supplemented with 10% FBS to 80% confluence. The day0 sample is ARPE19 cells at 80% confluence in serum supplemented DMEM.  For the rest of the samples, at 80% confluence the serum supplemented DMEM media was removed from the cultures and replaced with serum-free DMEM.  Cell culture continued until the indicated time point when the RNA was extracted from the cells.  Time points = day0, day1, day3, day4, day5, day6, and day9.

extract_protocol:
RNA was isolated from the confluent cultures on the appropriate day using Trizol™ (#15596-018, Invitrogen) as per manufacturer's instructions.  The starting volume of Trizol™ was 1.0ml. The RNA pellet was resuspended in 20µl H2O.  RNA concentration was measured using a NanoDrop 100.  RNA quality, as judged by RIN, was measured using an Agilent BioAnalyzer 2100 and RNA Nano Chips.  All the samples had RINs greater than 7.0.
Prepare one indexed library from polyA(+)-selected RNA for each sample, load pool on two lanes of HiSeq2000, run as Paired End 100 base reads.

tag: serum starvation day

value: Day 9


title: lckgfp_s061


title: Repeat3_Serum_Starved_Day6

value: Day 6


title: lckgfp_s059


title: lckgfp_s060


title: Repeat3_Serum_Starved_Day5

value: Day 5


title: lckgfp_s058


title: MV_CIITA_DC_3_RNAseq


title: Repeat3_Serum_Starved_Day4

value: Day 4


title: Repeat3_Serum_Starved_Day3

value: Day 3


title: lckgfp_s057

value: tail

value: 15 dpf


title: MV_CIITA_DC_1_RNAseq

value: Decitabine


title: MV_CIITA_DC_2_RNAseq

value: acute myeloid leukemia


title: lckgfp_s055


title: M13_Ctrl_IFN_2_RNAseq


title: Repeat3_Serum_Starved_Day1

value: Day 1


title: MV_CIITA_DMSO_1_RNAseq


title: Repeat3_Control_Day0

value: Day 0


title: lckgfp_s063


title: siHRP2-1

city: Tianjin

first: Bingxue

last: Lan

address: Qixiangtai road

country: China

institute: Tianjin Medical University

data_processing:
ATAC-seq data were processed according to ENCODE Processing Pipeline.
Clean reads were mapped to Mus musculus genome (mm10) by Bowtie2 (version 2.2.6)
Regions of enrichments were called using the MACS2 (version 2.1.1) peak caller.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated by deeptools

source_name: muscle

growth_protocol: C2C12 cells were cultured in DMEM medium supplemented with 20% fetal bovine serum (FBS).

extract_protocol:
Cells were resuspended in lysis buffer, centrifugated and resuspended for 60 min at 37℃ in Transposase reaction mix. The fragmented DNA was purified and added adaptor sequences by PCR. After DNA purification, DNA was sequenced on HiSeq X ten.
Construction of libraries were performed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme).

treatment_protocol: C2C12 cells were transfected with siRNAs against Hrp2/Dpf3a or control

value: muscle

value: myotube


title: Repeat2_Serum_Starved_Day5


title: siDPF3a-1


title: lckgfp_s053


title: lckgfp_s052


title: Repeat2_Serum_Starved_Day6


title: M13_Ctrl_DMSO_3_RNAseq


title: lckgfp_s054


title: sicontrol-1

value: sicontrol


title: M13_Ctrl_IFN_3_RNAseq

value: Control

value: IFNy


title: Repeat2_Serum_Starved_Day4


title: lckgfp_s051


title: MT-H3K36me2-IP

data_processing:
ChIP-seq data were processed according to ENCODE Processing Pipeline.
Clean reads were mapped to Mus musculus genome (mm10) by BWA (version 0.7.13)
Peaks were called using peak finding algorithm MACS2 (version 2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated by deeptools

extract_protocol:
For TY1,HRP2 and DPF3a ChIP, cells were double cross-linked with DMA and 1% formaldehyde. For H3K36me2 ChIP, cells were cross-linked with 1% formaldehyde. The crosslink was stopped by adding  2.5 M glycine. Cells were washed with PBS and harvested using ChIP lysis buffer. Cells were then sonicated to obtain fragments (100-500 bp) with Bioruptor Sonicator. Immunoprecipitation was performed withTY1, HRP2 (15134-1-AP), DPF3a and H3K36me2 (ab9049). After elution and reversal cross-linking, DNA was purified and sequenced on HiSeq X ten.
Construction of ChIP-seq library was performed using VAHTSTM Universal DNA Library Prep Kit for Illumina® V3  (Vazyme).

tag: chip antibody


title: M13_Ctrl_IFN_1_RNAseq

tag: cell line


title: siDPF3a-2


title: Repeat2_Serum_Starved_Day9


title: MV_CIITA_DCIFN_1_RNAseq

value: CIITA


title: M13_Ctrl_DCIFN_3_RNAseq


title: M13_Ctrl_DMSO_2_RNAseq

value: DMSO


title: lckgfp_s056


title: lckgfp_s048


title: Repeat2_Control_Day0


title: Repeat2_Serum_Starved_Day1


title: MT-TY1-HRP2-W21A-input


title: M13_Ctrl_DMSO_1_RNAseq


title: M13_Ctrl_DCIFN_1_RNAseq


title: MT-TY1-HRP2-IP

description: c2c12 myotube cells stably expressing TY1 tagged HRP2 was used to perform ChIP-seq with TY1 antibody

tag: genotype

value: stably expressing TY1 tagged HRP2


title: lckgfp_s049


title: M13_Ctrl_DCIFN_2_RNAseq


title: MT-TY1-HRP2-input

tag: cell type


title: M13_Ctrl_DC_3_RNAseq


title: Repeat1_Serum_Starved_Day9

value: Day 9


title: lckgfp_s047


title: M13_Ctrl_DC_2_RNAseq


title: Repeat2_Serum_Starved_Day3


title: lckgfp_s050


title: lckgfp_s045


title: MT-TY1-HRP2-W21A-IP

description: c2c12 myotube cells stably expressing TY1 tagged HRP2 W21A mutation was used to perform ChIP-seq with TY1 antibody


title: M13_Ctrl_DC_1_RNAseq


title: Repeat1_Serum_Starved_Day4

value: Day 4


title: M13_CIITA_IFN_3_RNAseq


title: MT-siHRP2-HRP2-input


title: MT-sicontrol-HRP2-IP

description: c2c12 myotube cells transiently transfected with scramble siRNA  was subjected to ChIP-seq with HRP2 antibody


title: Repeat1_Serum_Starved_Day6

value: Day 6


title: Repeat1_Control_Day0


title: MT-siHRP2-HRP2-IP

description: c2c12 myotube cells transiently transfected with HRP2 siRNA  was subjected to ChIP-seq with HRP2 antibody

value: transiently transfected with HRP2 siRNA


title: M13_CIITA_IFN_1_RNAseq


title: M13_CIITA_IFN_2_RNAseq


title: MT-sicontrol-HRP2-input


title: MT-siHRP2-DPF3a-input


title: lckgfp_s043

value: tail

value: 15 dpf


title: lckgfp_s046


title: M13_CIITA_DMSO_2_RNAseq

value: acute myeloid leukemia


title: M13_CIITA_DMSO_3_RNAseq


title: Repeat1_Serum_Starved_Day5

value: Day 5


title: lckgfp_s041


title: MT-siHRP2-DPF3a-IP

description: c2c12 myotube cells transiently transfected with HRP2 siRNA  was subjected to ChIP-seq with DPF3a antibody


title: lckgfp_s040


title: lckgfp_s042


title: M13_CIITA_DMSO_1_RNAseq


title: lckgfp_s044


title: lckgfp_s039


title: Repeat1_Serum_Starved_Day3

value: Day 3


title: Repeat1_Serum_Starved_Day1

value: Day 1


title: MT-sicontrol-DPF3a-input

value: muscle

value: myotube


title: Treg Mycfl/fl_rep4

type: RNA

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Six micrograms (6 ug) of cDNA was hybridized for 16h at 45C on a Mouse Gene 2.0 ST GeneChip array. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.5

label: biotin

source_name: Treg cells from Foxp3Cre mouse crossed with Mycfl/fl mouse

label_protocol: Sense target cDNA was prepared from twelve nanograms (12 ng) of total RNA using the Ovation WTA Pico v2 system (TECAN P/N 3302-60) and the Encore Biotin module (TECAN P/N 4200-60).

growth_protocol: CD4+Foxp3YFP+ Treg cells were sort-purified from pooled spleen and lymph nodes of Foxp3-Cre Myc fl/fl and WT control mixed bone marrow chimera mice

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

value: T regulatory cells

tag: genotype/variation

value: Foxp3-Cre Myc fl/fl


title: lckgfp_s038


title: lckgfp_s037


title: M13_CIITA_DCIFN_2_RNAseq

value: CIITA


title: MT-HRP2-IP


title: Treg WT_rep4

source_name: Treg cells from WT mouse

tag: strain

value: WT


title: M13_CIITA_DCIFN_3_RNAseq


title: MT-input


title: MT-DPF3a-IP


title: lckgfp_s035


title: M13_CIITA_DC_3_RNAseq

value: Decitabine


title: siHRP2-2


title: M13_CIITA_DCIFN_1_RNAseq


title: sicontrol-2

value: sicontrol


title: Treg Mycfl/fl_rep1


title: M13_CIITA_DC_2_RNAseq


title: Treg Mycfl/fl_rep2


title: Treg WT_rep3


title: MB-TY1-HRP2-IP

description: c2c12 myoblast cells stably expressing TY1 tagged HRP2 was used to perform ChIP-seq with TY1 antibody

value: myoblast

value: stably expressing TY1 tagged HRP2


title: lckgfp_s033


title: Treg Mycfl/fl_rep3


title: invitro_Pf2_011

city: Bentley

first: Darcy

middle: Adam Bain

last: Jones

state: Western Australia

address: Kent Street

department: Centre for Crop and Disease Management

country: Australia

institute: Curtin University

description: RNA was extracted from 3 day old cultures of P. nodorum in Fries 3 broth shaking at room temperature (approx 22^oC).

data_processing:
Read adapters were trimmed using cutadapt v1.12 (https://cutadapt.readthedocs.io/), cutadapt --minimum-length 25 -a "AGATCGGcutadapt AAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG" -A "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT" -g "AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" -G ""GTTCGTCTTCTGCCGTATGCTCTANNNNNNCACTGACCTCAAGTCTGCACACGAGAAGGCTAG -n 3 -o trimmed_R1.fastq.gz -p trimmed_R2.fastq.gz reads1.fastq.gz reads2.fastq.gz
Fastq read quality was assessed before and after trimming using FastQC v0.11.5 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Fungal reads were split from Wheat reads using BBSplit v36.67 (https://sourceforge.net/projects/bbmap) using the P. nodorum SN15 genome as bait (DOI: 10.1534/g3.112.004994). bbsplit.sh ambiguous=all path=index ref_SN15=genome.fasta out_SN15="split_R#.fastq.gz" outu="unaligned_R#.fastq.gz" in=reads1.fastq.gz in2=reads2.fastq.gz refstats=refstats.tsv scafstats=scafstats.tsv
Split fungal reads were aligned to the P. nodorum SN15 genome (DOI: 10.1534/g3.112.004994) using STAR v2.5.0a in 2 passes. The index was created including splice sites from existing annotations (DOI: 10.1371/journal.pone.0147221). STAR --runMode genomeGenerate --genomeDir mygenome  --genomeFastaFiles genome.fasta --sjdbGTFfile genes.gtf --sjdbOverhang 124 --genomeSAindexNbases 11
In the first STAR alignment pass, only splice junctions were retained. STAR --readFilesCommand zcat --genomeDir mygenome --outSAMtype None --outSAMmode None --outSJfilterReads All --outSJfilterOverhangMin 5 1 1 1 --outSJfilterCountUniqueMin 10 5 5 5 --outSJfilterDistToOtherSJmin 5 0 0 3 --outSJfilterIntronMaxVsReadN 0 1 500 5000 10000 20000 --alignIntronMin 5 --alignIntronMax 10000 --alignSJoverhangMin 1 --alignSJDBoverhangMin 1 --alignSoftClipAtReferenceEnds No --outFileNamePrefix mygenome reads1.fastq.gz reads2.fastq.gz
In the second STAR alignment pass, splice junctions from all first pass alignments were used as hints. STAR --readFilesCommand zcat --genomeDir mygenome --sjdbFileChrStartEnd *SJ.out.tab --outSAMtype BAM Unsorted --outBAMcompression 1 --outSJfilterReads All --outSJfilterCountUniqueMin 10 5 5 5 --outSJfilterIntronMaxVsReadN 0 1 500 5000 10000 20000 --alignIntronMin 5 --alignIntronMax 10000 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --alignSoftClipAtReferenceEnds No --outFilterType BySJout --outFilterMultimapNmax 1 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.2 --outMultimapperOrder Random --outSAMattributes All --outSAMstrandField intronMotif\ --outSAMattrIHstart 0 --outSAMmapqUnique 50 reads1.fastq.gz reads2.fastq.gz
BAM alignments were evaluated using samtools, RSeQC, and MultiQC.
Read counts were found using featureCounts v1.5.1 (http://subread.sourceforge.net/) using existing gene predictions (DOI: 10.1371/journal.pone.0147221). featureCounts -a genes.gtf -t exon -s 2 -p -B -C -o counts.tsv aligned.bam
Normalised fragment abundance was generated using DESeq2 v1.14.1 (DOI: 10.1186/s13059-014-0550-8) R package. The following sequence of functions/steps were used, with parameters affecting analysis indicated: `DESeqDataSetFromMatrix`; filter  genes with no fragments aligned; `estimateSizeFactors`; `DESeq(betaPrior=TRUE)` ; `rlog(blind = FALSE)`; `varianceStabilizingTransformation(blind = FALSE)`.
Genome_build: Parastagonospora nodorum SN15 genome, published but not in NCBI/INDSC [DOI: 10.1534/g3.112.004994,DOI:10.1371/journal.pone.0147221]. Available at: https://github.com/robsyme/Parastagonospora_nodorum_SN15
Supplementary_files_format_and_content: count_table.xlsx contains both the raw read counts from featureCounts and the DeSeq2 VST transformed counts for each of the 16 biological replicates, with gene location information.

organism: Parastagonospora nodorum

source_name: Mutant pf2-69 in vitro sample.

extract_protocol:
Total RNA was extracted using the Invitrogen TRIzol Plus RNA purification kit (cat: 12183A).
Libraries were constructed using an Illumina TruSeq stranded kit using poly-A pull down for mRNA enrichment, with a target insert size of 180 bp. Sequencing was performed on a HiSeq2500 v4 with 125bp PE reads. Both library construction and sequencing were performed by the Garvin Institute (Kinghorn Centre for Clinical Genomics/SCI Ramachiotti).

tag: culture

value: in vitro

tag: isolate


title: Treg WT_rep2


title: MB-TY1-HRP2-input


title: M13_CIITA_DC_1_RNAseq


title: lckgfp_s036

source_name: Danio rerio tail

tag: line

value: tail


title: M13_Ctrl_IFN_3_RRBS

description: RRBS of cells expressing indicated sgRNAs after 72 h treatment with decitabine (100 nM) and/or recombinant human interferon gamma (100 ng/ml) or DMSO.

data_processing:
Basecalls performed using standard Illumina base-caller
Poor quality and adapter containing bases were trimmed using TrimGalore in RRBS mode using stringency 3
Reads were mapped to the human genome (hg38 v2) using Bismark
Mapped reads were processed with Bismark methylation caller to estimate the methylation status of each cytosine in every mapped read
Genome_build: hg38
Supplementary_files_format_and_content: Bismark Coverage report in a GZIP compressed format. Columns: 1) chromosome, 2) genomic start position, 3) genomic end position, 4) percetange of methylation at that position, 5) number of C bases that are methylated, 6) number of C bases that are unmethylated

extract_protocol:
DNA was extracted using NucleoSpin Tissue kit (Macherey-Nagel). The following QC and library construction steps wer performed at Novogene. Agarose Gel Electrophoresis was run to test DNA degradation and potential RNA contamination. Qubit 2.0 was used to quantify DNA concentration.
After the DNA sample QC, positive control DNAs were added into the samples, and then they were fragmented into 200-400 bp using Covaris S220. Next, terminal repairing, A-ligation, and methylation sequencing adapters ligation were performed to the obtained DNA fragments. The final DNA library was obtained after bisulfite treatment (EZ DNA Methylation Gold Kit, Zymo Research), size selection, and PCR amplification steps. Library concentration was firstly quantified by Qubit 2.0. Then, the libraries were diluted to 1ng/µl before checking insert size on Agilent 2100 and quantified with higher accuracy by Q-PCR (effective concentration of library >2nM). After passing the library QC, different libraries were be pooled together and then fed into Illumina devices (Illumina Novaseq 6000) according to effective concentration and expected data volume. The sequencing strategy was paired-end sequencing 150 bp.

treatment_protocol: Cells were plated on 6-well plates at 1.5 million cells/well in a volume of 3 ml and treated with 100 nM decitabine (Selleck) or DMSO as a control, both in the presence or absence of 100 ng/ml recombinant human interferon gamma (Peprotech). After 3 days, the cultures were washed with PBS and 50% of the cells were harvested for DNA extraction.

value: Control

value: IFNy


title: MT-DPF3a-input

tag: tissue


title: Treg WT_rep1


title: M13_Ctrl_IFN_2_RRBS

value: acute myeloid leukemia


title: lckgfp_s031

tag: devlopmental stage

value: 15 dpf


title: invitro_Pf2_010


title: invitro_Pf2_009


title: lckgfp_s030


title: M13_Ctrl_IFN_1_RRBS

tag: cancer type


title: MB-HRP2-input


title: invitro_SN15_003

source_name: Wild type SN15 in vitro sample.


title: MT_siHrp2_rep1

data_processing:
FastQC (version 0.11.8) was used to do quanlity control checks on clean reads.
The expression of genes was quantified by Salmon (version 0.8.0) with default parameters.
DEGs (differential expressed genes) between samples were generated by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: TPM for each sample.

extract_protocol:
Total RNA isolation was performed using TRIzol (Invitrogen). Total RNAs from cultured cells were subjected to Oligo dT selection and adaptor ligation.
Construction of RNA-seq library was completed by BGI company (Shenzhen,China).

treatment_protocol: C2C12 cells were transfected with siRNAs against Hrp2/Dpf3a/Brg1 or control.


title: M13_Ctrl_DMSO_2_RRBS

tag: sgrna

value: DMSO


title: lckgfp_s028

data_processing:
STAR (2.5)
Htseq (0.8.0) htseq-count -m intersection-nonempty --nonunique all
Genome_build: GRCz10
Supplementary_files_format_and_content: Raw counts of numbers of reads aligned to each feature for each cell, in tab-separated format (lckgfp_counts.txt)

extract_protocol:
Lysis was performed as described in Schaum et al., Nature 2018
A Smart-Seq2 based protocol was used for reverse transcription and cDNA amplification, and a Nextera based protocol was used for library preparation, as described in Schaum et al., Nature 2018


title: M13_Ctrl_DMSO_3_RRBS

tag: treatment


title: lckgfp_s034


title: lckgfp_s029


title: invitro_Pf2_008


title: MT_siDpf3a_rep2

value: muscle


title: invitro_SN15_002


title: MT_siDpf3a_rep1

value: myotube


title: MB-HRP2-IP


title: lckgfp_s027


title: lckgfp_s032


title: M13_Ctrl_DMSO_1_RRBS

tag: replicate


title: invitro_SN15_001


title: lckgfp_s026


title: M13_Ctrl_DCIFN_3_RRBS


title: MT_siHrp2_rep2


title: lckgfp_s025


title: MT_siBrg1_rep1


title: M13_Ctrl_DCIFN_2_RRBS


title: invitro_SN15_000


title: lckgfp_s024


title: MT_siBrg1_rep2


title: M13_Ctrl_DCIFN_1_RRBS


title: MT_siCtrl_rep2

value: siCtrl


title: M13_Ctrl_DC_3_RRBS


title: MT_siCtrl_rep1


title: M13_Ctrl_DC_2_RRBS


title: MB_siCtrl_rep2


title: lckgfp_s022


title: lckgfp_s023


title: M13_Ctrl_DC_1_RRBS


title: hetIL-15_6

first: Maggie

middle: C

last: Cam

address: Bldg 37, Rm 1136A, 37 Convent Drive

department: NCI

institute: NIH

description: nCounter PanCancer Immune Profiling Panel (NanoString Technologies) was used to monitor the expression of a panel of 770 genes related to immune-oncology in MC38 tumors of PBS- and hetIL-15-treated mice. Tumors wereanalyzed 3 hours after the 4th administration

scan_protocol: The mRNA molecules were counted with the NanoString nCounter at the Laboratory of Molecular Technology (Advance Technology Program, Frederick National Laboratory)

data_processing: Analysis was performed with a workflow written in R and through a user interface developed on the Foundry Platform (Palantir Technologies). Raw data were filtered to remove low expressed genes, leaving 758 genes out of the original 780. To define differentially expressed genes, we run limma and set thresholds at 2-fold change and p<0.05 difference between groups (adjusted p value following Bonferroni multiple comparison testing).  Gene enrichment analysis on the GO database was subsequently performed on the top 150 genes (sorted by t-statistic) using the Fisher’s Exact Test (https://github.com/CCBR/l2p).

label: nanostring oligonucleotide probe

source_name: MC38 tumor

label_protocol: Labeled according to the manufacturer's protocol.

growth_protocol: MC38 colon carcinoma cells were maintained in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS, Sigma), penicillin/streptomycin, essential amino acids and HEPES.  Six to eight-week old animals received 1-2x105 tumor cells by subcutaneous (SC) injection in the flank

extract_protocol: Tumors (3 hours after 4th injections) were excised, mechanically disrupted in RLT buffer (QIAGEN) using 2.8 mm ceramic beads (Precellys Lysing kit) and Precellys Evolution Homogenizer. RNA extraction was performed with RNeasy (QIAGEN) including on-column DNase I digestion, according to the manufacturer’s instructions

treatment_protocol: Five days after inoculation of tumor cells, tumor-bearing mice were randomized into two groups, PBS and hetIL-15 treated. hetIL-15 was purified from HEK293 cells (Admune Therapeutic LLC/Novartis). For hetIL-15 treatment, mice received intraperitoneal (IP) injection of 3 μg (molar mass of IL-15) of hetIL-15 [53, 65] 3 times/week for a total of 4 injections.


title: hetIL-15_5

hyb_protocol: nCounter PanCancer Immune Profiling Panel (NanoString Technologies) was used to monitor the expression of a panel of 770 genes related to immune-oncology


title: hetIL-15_4


title: MB_siCtrl_rep1


title: lckgfp_s021


title: M13_CIITA_IFN_3_RRBS


title: lckgfp_s020


title: CO2+1-MCP 4dC

city: hangzhou

first: Wei

last: Wu

address: yuhangtang road 866

institute: zhejiang university

data_processing:
Through in-house perl scripts, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set default.
Gene expression levels were estimated by RSEM (Li et al, 2011).
Supplementary_files_format_and_content: fasta file contains the sequences of all unigenes; xls files include annotation for each unigene, or readcount and FPKM values for each Sample

organism: Diospyros kaki

source_name: flesh

extract_protocol:
CTAB was used to extract total RNA
cDNA was prepared for sequencing using standard Illumina protocols

tag: days after storage


title: hetIL-15_3


title: lckgfp_s019


title: CO2+1-MCP 4dB


title: hetIL-15_2


title: hetIL-15_1


title: M13_CIITA_IFN_2_RRBS


title: lckgfp_s018


title: M13_CIITA_IFN_1_RRBS


title: CO2+1-MCP 4dA


title: lckgfp_s017


title: M13_CIITA_DMSO_3_RRBS


title: Control_4

value: PBS


title: Control_5


title: CO2+1-MCP 1dC


title: M13_CIITA_DMSO_2_RRBS

value: CIITA


title: CO2+1-MCP 1dB


title: lckgfp_s015


title: CO2+1-MCP 1dA


title: lckgfp_s016


title: lckgfp_s014


title: CO2 4dC

value: high CO2


title: Control_2


title: Control_3


title: M13_CIITA_DCIFN_2_RRBS


title: lckgfp_s013


title: Control_1


title: lckgfp_s012


title: M13_CIITA_DCIFN_1_RRBS


title: CO2 4dA


title: M13_CIITA_DC_3_RRBS

value: Decitabine


title: lckgfp_s011


title: M13_CIITA_DC_2_RRBS


title: CO2 1dC


title: lckgfp_s010


title: CO2 1dB


title: M13_CIITA_DMSO_1_RRBS


title: M13_CIITA_DC_1_RRBS


title: lckgfp_s009


title: CO2 1dA


title: CO2 4dB


title: CK 4dC

value: control


title: lckgfp_s007


title: FUS-/-:FUS rep3

city: Madison

first: WEIYAN

last: JIA

state: WI

address: 1111 Highland Ave., 3068 WIMR

department: Department of Human Oncology

institute: University of Wisconsin- Madison

data_processing:
Raw reads adapters were trimmed by fastp( 0.19.7) with default setting
mapped to human genome(GRCh38) by STAR(2.7.0b)
The numbet of RNA-Seq reads mapped to each transcript were summarized with featureCounts(v1.6.3)
differential expression was called using DESeq2(1.22.2)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw or normalized reads for each Sample

source_name: U-2 OS

growth_protocol: U-2 OS and U-2 OS derivative cell lines were grown in McCoy’s medium(Cellgro, 10-050-CV) with 10% fetal bovine serum(Atlanta biologicals, S11150) and 1% Penicillin/Streptomycin(Corning, 30-002-CI). Cells were cultured at 37oC in 5% CO2.

extract_protocol:
Total RNA was isolated using the TRIzol reagent(Invitrogen, 15596018) following the manufacturer’s protocol and treated with TURBO Dnase(Invitrogen, AM2239).
RNA samples were sent to Novogene(Novogene Co., Ltd, Sacramento, CA) for non-stranded cDNA library building


title: FUS-/-:FUS rep2


title: CK 4dB


title: M13_CIITA_DCIFN_3_RRBS


title: FUS-/-:FUS rep1


title: CK 4dA


title: FUS-/- rep3


title: CK 1dC


title: lckgfp_s005

first: Elizabeth

last: Jerison

address: 529 E 57th St

institute: University of Chicago


title: lckgfp_s004


title: CK 1dB


title: FUS-/- rep2


title: FUS-/- rep1


title: Sham-2

city: Dalian

first: Qiuyue

last: Lin

address: No. 193, Lianhe Road, Dalian

department: First Affliated Hospital of Dalian Medical University

hyb_protocol: A Gene Chip Fluidics Station 450 was used to wash and stain the cells.

scan_protocol: A Gene Chip 3000 7G scanner was used to measure the fluorescence signal.

data_processing: The CEL files of each signal value of the gene probe were generated by using GCOS software. mRNA expression profiling was performed by using a mouse Genome 430 2.0 Array (Affymetrix Gene Chip, USA) according to the manufacturer’s instructions.

source_name: MLECs with saline

label_protocol: RNA was biotin-labeled after evaluating RNA quality and integrity and placed on a Gene Chip Hybridization Oven 645 instrument.

growth_protocol: Mouse LECs were grown in DMEM basic medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin in an atmosphere of 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted from the cells by using TRIzol (Invitrogen, United States) according to the manufacturer’s instructions.

treatment_protocol: For in vitro cell assays and gene expression profile analysis, LECs were stimulated by angiotensin II (Ang II, A9525, Sigma) at a dose of 500 nM in culture medium for 12 and 24 hours, respectively.

value: murine lymphatic endothelial (MLECs) cell line

value: saline


title: lckgfp_s008


title: Sham-5

institute: First Affliated Hospital of Dalian Medical University


title: Sham-3


title: lckgfp_s003


title: AII-24-3

source_name: MLECs with AII 24h

value: Ang II (500 nM) 24h


title: AII-24-5


title: CK 1dA


title: Sham-1


title: Sham-4


title: CK 0dC


title: lckgfp_s002

value: tail


title: AII-24-2


title: AII-24-1


title: AII-24-4


title: FUS+/+ rep2


title: MT-sicontrol-DPF3a-IP

description: c2c12 myotube cells transiently transfected with scramble siRNA  was subjected to ChIP-seq with DPF3a antibody


title: lckgfp_s001


title: CK 0dB


title: lckgfp_s000


title: FUS+/+ rep1


title: AII-12-5

source_name: MLECs with AII 12h

value: Ang II (500 nM) 12h


title: AII-12-3


title: AII-12-4


title: CK 0dA


title: AII-12-2


title: FUS+/+ rep3


title: AII-12-1


title: lckgfp_s006


title: E915N

status: Public on May 12 2020

first: Howard

last: Yang

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

description: frozen tissue extracted by Trizol

hyb_protocol: For mRNA array, total RNA was reverse transcripted to cDNA, reverse transcripted to labelled aRNA, purified, fragmented, and hybridized to each array chip according to the manufacturer's instructions.

scan_protocol: The mRNA arrays were washed using Affymetrix fluidics stations, and scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Microarray data were normalized using the RMA method .

label: Biotin

source_name: adjacent normal tissue

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: Two methods were used to extract total RNA. One is by standard Trizol method and Second is by AllPrep DNA/RNA/Protein Mini Kit from QIAGEN. After extractiong, all are followed with qualification check by Agilent 2100.

value: adjacent normal tissue


title: E972N

description: frozen tissue extracted by Trizol


title: E925N

description: frozen tissue extracted by Trizol


title: E939T

description: frozen tissue extracted by Trizol

source_name: tumor tissue

value: tumor tissue


title: E942T

description: frozen tissue extracted by Trizol


title: E921T

description: frozen tissue extracted by Trizol


title: E921N

description: frozen tissue extracted by Trizol


title: E973T

description: frozen tissue extracted by Trizol


title: E887T

description: frozen tissue extracted by Trizol


title: E939N

description: frozen tissue extracted by Trizol


title: E942N

description: frozen tissue extracted by Trizol


title: E863T

description: frozen tissue extracted by Trizol


title: E863N

description: frozen tissue extracted by Trizol


title: E915T

description: frozen tissue extracted by Trizol


title: E941T

description: frozen tissue extracted by Trizol


title: E868N

description: frozen tissue extracted by Trizol


title: E941N

description: frozen tissue extracted by Trizol


title: E978N

description: frozen tissue extracted by Trizol


title: E864N

description: frozen tissue extracted by Trizol


title: E925T

description: frozen tissue extracted by Trizol


title: E945T

description: frozen tissue extracted by Trizol


title: E945N

description: frozen tissue extracted by Trizol


title: E848T

description: frozen tissue extracted by Trizol


title: E868T

description: frozen tissue extracted by Trizol


title: E972T

description: frozen tissue extracted by Trizol


title: E887N

description: frozen tissue extracted by Trizol


title: E978T

description: frozen tissue extracted by Trizol


title: E864T

description: frozen tissue extracted by Trizol


title: E848N

description: frozen tissue extracted by Trizol


title: E973N

description: frozen tissue extracted by Trizol


title: E844T

description: frozen tissue extracted by Trizol


title: E809N

description: frozen tissue extracted by Trizol


title: E822T

description: frozen tissue extracted by Trizol


title: E782N

description: frozen tissue extracted by Trizol


title: E844N

description: frozen tissue extracted by Trizol


title: E781N

description: frozen tissue extracted by Trizol


title: E822N

description: frozen tissue extracted by Trizol


title: E809T

description: frozen tissue extracted by Trizol


title: E381T

description: frozen tissue extracted by Trizol


title: E842N

description: frozen tissue extracted by Trizol


title: E782T

description: frozen tissue extracted by Trizol


title: E362T

description: frozen tissue extracted by Trizol


title: E796T

description: frozen tissue extracted by Trizol


title: E1490N

description: frozen tissue extracted by Trizol


title: E746T

description: frozen tissue extracted by Trizol


title: E842T

description: frozen tissue extracted by Trizol


title: E796N

description: frozen tissue extracted by Trizol


title: E742T

description: frozen tissue extracted by Trizol


title: E379N

description: frozen tissue extracted by Trizol


title: E746N

description: frozen tissue extracted by Trizol


title: E362N

description: frozen tissue extracted by Trizol


title: E410N

description: frozen tissue extracted by Trizol


title: E379T

description: frozen tissue extracted by Trizol


title: E1490T

description: frozen tissue extracted by Trizol


title: E381N

description: frozen tissue extracted by Trizol


title: E781T

description: frozen tissue extracted by Trizol


title: E1463T

description: frozen tissue extracted by Trizol


title: E742N

description: frozen tissue extracted by Trizol


title: E410T

description: frozen tissue extracted by Trizol


title: E1408N

description: frozen tissue extracted by Trizol


title: E1463N

description: frozen tissue extracted by Trizol


title: E1164T

description: frozen tissue extracted by Trizol


title: E1405N

description: frozen tissue extracted by Trizol


title: E1405T

description: frozen tissue extracted by Trizol


title: E892T

description: frozen tissue extracted by AllPrep DNA/RNA/Protein Mini kit from GIAGEN

data_processing: The expression data were normalized by RMA using the software Affymetrix Expression Console, version 1.2.1.


title: E1301T

description: frozen tissue extracted by Trizol


title: E948N


title: E1301N

description: frozen tissue extracted by Trizol


title: E892N


title: E948T


title: E1879T


title: E1880T


title: E387N


title: E1164N

description: frozen tissue extracted by Trizol


title: E1408T

description: frozen tissue extracted by Trizol


title: E1885N


title: E1875T


title: E1877N


title: E1882N


title: E387T


title: E891T


title: E1880N


title: E2644T


title: E1885T


title: E891N


title: E1874T


title: E1879N


title: E1882T


title: E1864T


title: E1875N


title: E1864N


title: E1877T


title: E1796T


title: E1866N


title: E1793T


title: E1866T


title: E1796N


title: E1860T


title: E1862T


title: E1874N


title: E2644N


title: E1709N


title: E1756N


title: E1709T


title: E1782N


title: E1793N


title: E1635T


title: E1862N


title: E1629T


title: E1756T


title: E1782T


title: E1633N


title: E1628T


title: E1635N


title: E1629N


title: E1860N


title: E1627N


title: E1633T


title: E1628N


title: E1627T


title: E1603N


title: E1603T


title: E1614N


title: E1610T


title: E1589T


title: E1589N


title: E1584T


title: E1576N


title: E1575N


title: E1577T


title: E1578T


title: E1578N


title: E1610N


title: E1573N


title: E1572N


title: E1584N


title: E1573T


title: E1572T


title: E1577N


title: E1558T


title: E1575T


title: E1566T


title: E1566N


title: E1551T


title: E1556T


title: E1546N


title: E1535T


title: E1542T


title: E1556N


title: E1532T


title: E1551N


title: E1535N


title: E1478N


title: E1546T


title: E1507N


title: E1521T


title: E1520T


title: E1498T


title: E1510T


title: E1520N


title: E1475T


title: E1517T


title: E1507T


title: E1498N


title: E1510N


title: E1521N


title: E1451T


title: E1542N


title: E1517N


title: E1532N


title: E1451N


title: E1478T


title: E1475N


title: E1450N


title: E1450T


title: E1447T


title: E1447N


title: E1558N


title: E1440T


title: E1400N


title: E1400T


title: E1440N


title: E1242T


title: E1242N


title: E1423T


title: E1415N


title: E1293N


title: E1416N


title: E1270N


title: E1415T


title: E1435T


title: E1416T


title: E1241T


title: E1435N


title: E1270T


title: E1256N


title: E1250N


title: E1423N


title: E1293T


title: E1256T


title: E1241N


title: E1195T


title: E1210T


title: E1614T


title: E1187T


title: E1195N


title: E1187N


title: E1163T


title: E1210N


title: TAM_4days_WT_S15221

city: Milan

first: Marco

last: Filipuzzi

address: Via Giuseppe Ripamonti, 435

country: Italy

institute: IEO

description: WT

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v -i
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Genome_build: Genome_build: mm9
Supplementary_files_format_and_content: txt file reporting the eRPKM, log2FC and padj from DESEq2 output

source_name: primary liver

extract_protocol:
Liver tissue was homogenized with GentleMACS M Tubes (Miltenyi Biotech, #130-096-335) and gentleMACS™ Dissociator (Miltenyi Biotech, #130-093-235) in RNA lysis buffer (Zymo, #R1054), and total RNA was purified from these lysates onto Quick-RNA Miniprep columns (Zymo, #R1054) and treated on-column with DNaseI. RNA quality was checked with the Agilent 2100 Bioanalyser (Agilent Technologies).
0.5-1 µg of RNA were used to prepare libraries for RNA-Seq with the TruSeq stranded total RNA Sample Prep Kit (Illumina, #20020596) following manufacturer instruction. RNA-seq libraries were then run on the Agilent 2100 Bioanalyser (Agilent Technologies) for quantification and quality control and then sequenced on Illumina NovaSeq or Illumina 2000 as detailed below.
Strand Specific RNA-Seq

treatment_protocol: For short-term liver-specific activation of the various alleles, 10^11 AAV8-TBG-CRE particles were given to 6- to 8-week-old mice and mice sacrificed after 4 days,

value: Liver

value: WT

tag: treatment protocol

value: 4-OHT 20 mg/mg 4-OHT i.p. 4days


title: E1179T


title: TAM_4days_WT_S15220

description: WT


title: TAM_4days_WT_S15219

description: WT


title: TAM_4days_WT_S14313

description: WT


title: Islets of β cell specific furin knockout mice (RIP-Cre+/- furin flox/flox), biological rep 4

city: Leuven

first: John

last: Creemers

address: ON I Herestraat 49 - box 607

department: Department of Human Genetics

country: Belgium

institute: KU Leuven

description: normal chow-fed animals

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45 degrees Celsius on Mouse gene 1.0ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned using the Affymetrix genechip scanner 3000.

data_processing: The data were normalized using RMA-sketch.

source_name: pancreatic islets

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (Label assay manual version4 701880Rev4, 2008, Affymetrix).

extract_protocol: Total RNA was extracted using the absolutely RNA microprep kit from Stratagene/Agilent.

tag: gender

value: male

tag: age

value: 12 weeks old

value: pancreatic islets

value: β cell specific furin knockout


title: TAM_4days_WT_S14312

description: WT

tag: genotype


title: Islets of β cell specific furin knockout mice (RIP-Cre+/- furin flox/flox), biological rep 3

description: normal chow-fed animals


title: TAM_4days_WT_S14311

description: WT

tag: cell type


title: E1576T


title: TAM_4days_WT_S14310

description: WT


title: Islets of β cell specific furin knockout mice (RIP-Cre+/- furin flox/flox), biological rep 2

description: normal chow-fed animals


title: Tum_MYC_EX3_209859

source_name: primary liver noduli

value: Liver Noduli


title: Tum_MYC_207155


title: Tum_MYC_205931


title: Tum_MYC_EX3_205779


title: Islets of control mice (furin flox/flox), biological rep 3

description: normal chow-fed animals


title: Tum_MYC_198825


title: E1163N


title: PRC1_GV_Ring1.SKO_rep3

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

description:
re-analysis of GSM3851719
PRC1_GV_Oocyte_GENES_ReadCounts.txt.gz

data_processing:
Spliced alignment of RNA-Seq data to a custom genome which contained M.musculus genome assembly (GRCm38/mm10 Dec. 2011) and ERCC92 sequences was done using STAR (version 2.5.0a, Dobin et al. 2013) with parameters "-outFilterMultimapNmax 300 -outMultimapperOrder Random -outSAMmultNmax 1 -alignIntronMin 20 -alignIntronMax 1000000", allowing multimappers with up to 300 matches in the genome and choosing positions for multimappers randomly.
Genome_build: mm10 + ERCC92
Supplementary_files_format_and_content: bigWig files for bins of 100 bp were generated by QuasR package (version 1.22.0) using only uniquely  mapped reads (minimum mapping quality mapqMin=255) and  the output values in the bigWig files were linearly scaled such that the total number of aligned reads per sample is 1e+6 (parameter scaling=1e+6).
Supplementary_files_format_and_content: Read count table (TXT file) for each gene in TxDb.Mmusculus.UCSC.mm10.knownGene (version 3.4.4) was created by qCount function in QuasR package selecting only uniquely  mapped reads.

source_name: GV-oocyte

growth_protocol: Ring1−/−; Rnf2f/f mice with or without Zp3-cre were maintained as described in Posfai et al. 2012 (PMID:22499591)

extract_protocol:
For RNA isolation, 15 GV oocytes from one mouse were pooled and RNA was extracted using the RNAEasy Micro Kit (Qiagen,74004) according to the manufacturer’s instructions. Total RNA was quantified and checked for quality on Agilent’s BioAnalyzer using the RNA 6000 Pico Kit (Agilent, 5067-1513).
RNA was amplified and converted to cDNA using the Ovation v2 Kit (NuGen, 7102). Sequencing libraries were prepared with the Truseq DNA LT kit (Illumina, FC-121-2001) and multiplexed, barcoded libraries were sequenced on an Illumina HiSeq instrument.

treatment_protocol: Cumulus oocyte complexes were isolated from ovaries of approx. 3 months old females. Granulosa cells were removed by repeated pipeting using a fine-pulled capilary glass needle in M2 medium. Oocytes were washed twice in M2 medium and subsequently washed twice in DNA suspension Buffer (TEKnova, PNT0221).

tag: strain background

value: mixed FVB, 129/Sv and C57BL/6J

value: Ring1 -/-; Rnf2 f/f

tag: tissue/cell type

value: germinal vesicle (GV) stage mouse oocytes


title: PRC1_GV_Ring1.SKO_rep2

description:
re-analysis of GSM3851718
PRC1_GV_Oocyte_GENES_ReadCounts.txt.gz


title: PRC1_GV_Ring1.SKO_rep1

description:
re-analysis of GSM3851717
PRC1_GV_Oocyte_GENES_ReadCounts.txt.gz


title: Islets of control mice (furin flox/flox), biological rep 2

description: normal chow-fed animals

tag: strain

value: control


title: Islets of β cell specific furin knockout mice (RIP-Cre+/- furin flox/flox), biological rep 1

description: normal chow-fed animals


title: iTreg_Input_ChIP-seq

city: Cambridge

first: Mohammed-Firas

last: Sadiyah

address: The Old Schools, Trinity Ln

country: United Kingdom

institute: University of Cambridge

data_processing:
The sequenced reads were aligned to the mouse genome (NCBIM37/mm9) with Bowtie 0.12.9; only uniquely mapped reads were retained
Peaks were called based on enrichment of ChIP-Seq reads over input reads (binomial distribution FDR < 5%)
Genome_build: mm9
Supplementary_files_format_and_content: MACS bed file, narrowPeak

source_name: Treg cells

extract_protocol:
Total CD4+ T cells were MACS-enrichment and FACS-sorted.
Cells were then transferred to a 96-well plate coated with anti-CD3ε and antiCD28 antibodies and cultured in RPMI complete media supplemented with TGF-β for 4 days.
2 x 107 cells were chemically crosslinked and sonicated on a Branson 450-D sonicator to generate fragmented genomic DNA
Chromatin immunoprecipitation was performed using the following antibodies: anti-BACH2 (N-2; Tohoku University), anti-JunD (sc-74; Santa Cruz) and (sc-586; Santa Cruz)
For sequencing of immunoprecipitated DNA, DNA fragments were blunt-end ligated to Illumina adaptors, amplified, and sequenced by using the HiSeq 2000 platform (Illumina)

value: spleen

value: post natal 8–12 weeks

value: wild type


title: PRC1_GV_Ring1.Rnf2.DKO.Zp3_rep2

description:
re-analysis of GSM3851715
PRC1_GV_Oocyte_GENES_ReadCounts.txt.gz

value: Ring1 -/-; Rnf2 f/f; Zp3-cre


title: iTreg_JunD_ChIP-seq


title: PRC1_GV_Ring1.Rnf2.DKO.Zp3_rep1

description:
re-analysis of GSM3851714
PRC1_GV_Oocyte_GENES_ReadCounts.txt.gz


title: iTreg_BACH2_ChIP-seq


title: Islets of control mice (furin flox/flox), biological rep 1

description: normal chow-fed animals


title: E1179N

value: adjacent normal tissue


title: BJ-T-AKT2

city: Melbourne

first: Keefe

middle: T

last: Chan

state: VIC

address: 305 Grattan St

department: Division of Cancer Research

institute: Peter MacCallum Cancer Centre

data_processing:
The quality of the generated 50bp paired-end reads was assessed with FastQC 0.11.2.
Adapters were trimmed using Cutadapt v1.7
Reads were mapped to the human reference genome (hg19/GRCh37) using TopHat2 (version 2.0.13)/Bowtie2 (version 2.2.3.0)
Picard 1.125 was used to generate BAM indices and to calculate insert size.
Samtools 0.1.18 was used to sort and merge.
featureCounts (v1.6.2) was used to count the number of reads per gene with ENSEMBL GTF v87
Genome_build: hg19
Supplementary_files_format_and_content: csv file includes normalized counts for each sample

source_name: BJ-TERT fibroblasts

growth_protocol: BJ-TERT cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) + 20 mM HEPES, 17% Medium 199, 15% fetal bovine serum (FBS), and 1% GlutaMAXTM L-alanyl-L-glutamine dipeptide at 37°C under 5% CO2.

extract_protocol:
Total RNA was extracted using the Qiagen Rneasy Mini Kit as per the manufacturer's instructions.
RNA libraries were prepared for sequencing according to standard Illumina protocols (TruSeq RNA Sample Preparation Guide v2 Guide).

treatment_protocol: BJ-TERT cells were untreated or transduced with pBabe-puro-myrAKT1 and RNA-seq was performed using total RNA extracted from triplicate samples on Day 6 post-transduction.

value: replicate 2

tag: timepoint

value: 6 days


title: BJ-T-AKT1

value: replicate 1


title: Islets of control mice (furin flox/flox), biological rep 4

description: normal chow-fed animals

value: male


title: BJ-T-AKT3

value: replicate 3


title: E1250T

value: tumor tissue


title: BJ-T3

value: non-transduced


title: Tum_MYC_EX3_205929

value: Liver Noduli


title: BJ-T1


title: BJ-T2


title: PRC1_GV_Ring1.Rnf2.DKO.Zp3_rep3

description:
re-analysis of GSM3851716
PRC1_GV_Oocyte_GENES_ReadCounts.txt.gz

value: mixed FVB, 129/Sv and C57BL/6J


title: Alveolar macrophage TB Control replicate 5

city: Medellín

first: LELIA

last: LAVALETT

state: Antioquia

department: Antioquia

country: Colombia

institute: Universidad de antioquia

description:
replicate 1
Sample 50

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were extracted with Illumina GenomeStudio v2011.1  software. Probes signal value was transformed by logarithm and normalized by Z-ratio method. The data were normalised using quantile normalisation with Lumi package in R

source_name: Human alveolar macrophage

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: bronchoalveolar lavage

tag: tb strain

value: Mtb UT127

value: Infection 1


title: Alveolar macrophage TB Infection 2 replicate 1

description:
replicate 3
Sample 57

tag: tissue

value: Mtb UT205

value: Infection 2


title: Alveolar macrophage healthy Infection 2 replicate 1

description:
replicate 3
Sample 75


title: Alveolar macrophage TB Infection 1 replicate 5

description:
replicate 1
Sample 51


title: Alveolar macrophage TB Infection 1 replicate 3

description:
replicate 4
Sample 59


title: Alveolar macrophage TB Infection 2 replicate 2

description:
replicate 4
Sample 60


title: Alveolar macrophage TB Infection 2 replicate 3

description:
replicate 5
Sample 81


title: Alveolar macrophage healthy Infection 1 replicate 5

description:
replicate 1
Sample 66


title: Alveolar macrophage TB Control replicate 2

description:
replicate 2
Sample 55

value: TB control


title: Alveolar macrophage TB Infection 1 replicate 4

description:
replicate 5
Sample 80


title: Alveolar macrophage TB Infection 1 replicate 1

description:
replicate 2
Sample 53


title: Alveolar macrophage TB Control replicate 1

description:
replicate 1
Sample 52


title: Alveolar macrophage TB Infection 1 replicate 6

description:
replicate 2
Sample 54


title: Alveolar macrophage healthy Infection 1 replicate 4

description:
replicate 5
Sample 77


title: Alveolar macrophage healthy Control replicate 3

description:
replicate 3
Sample 73

value: Healthy control


title: Alveolar macrophage TB Control replicate 4

description:
replicate 4
Sample 61


title: Alveolar macrophage healthy Infection 1 replicate 6

description:
replicate 2
Sample 72


title: Alveolar macrophage healthy Control replicate 4

description:
replicate 4
Sample 76


title: Alveolar macrophage TB Control replicate 3

description:
replicate 3
Sample 58


title: Alveolar macrophage healthy Control replicate 5

description:
replicate 1
Sample 65


title: Alveolar macrophage healthy Infection 1 replicate 2

description:
replicate 3
Sample 71


title: splenic macrophage Infection 2 replicate 3

description:
replicate 3
Sample 9

source_name: Human splenic macrophage

value: spleen slices from deceased donor


title: Alveolar macrophage healthy Infection 1 replicate 1

description:
replicate 2
Sample 68


title: Alveolar macrophage TB Infection 1 replicate 2

description:
replicate 3
Sample 56


title: Alveolar macrophage healthy Control replicate 1

description:
replicate 1
Sample 64


title: Alveolar macrophage healthy Control replicate 2

description:
replicate 2
Sample 70


title: Alveolar macrophage healthy Infection 1 replicate 3

description:
replicate 4
Sample 74


title: splenic macrophage Infection 2 replicate 6

description:
replicate 6
Sample 18


title: splenic macrophage Infection 2 replicate 5

description:
replicate 5
Sample 15


title: splenic macrophage Infection 2 replicate 4

description:
replicate 4
Sample 12


title: splenic macrophage Control replicate 5

description:
replicate 5
Sample 16

value: Control


title: splenic macrophage Infection 1 replicate 2

description:
replicate 2
Sample 5


title: splenic macrophage Infection 1 replicate 4

description:
replicate 4
Sample 11


title: splenic macrophage Infection 1 replicate 1

description:
replicate 1
Sample 2


title: splenic macrophage Control replicate 2

description:
replicate 2
Sample 4


title: splenic macrophage Infection 1 replicate 5

description:
replicate 5
Sample 14


title: splenic macrophage Infection 1 replicate 6

description:
replicate 6
Sample 17


title: T47D_WT_basal_batch1_3

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

institute: The Institute of Cancer Research

scan_protocol: Standard Illumina scanning protocol of iScan

data_processing: The data were divided into subsets according to the groups being compared; only the samples involved in a given comparison are used. Subsets were then filtered to remove any non-expressed probes using the detection p-value from Illumina. Across all samples in each subset probes for which the intensity values were not significantly different (p>0.01) from the negative controls were removed from the analysis. Following filtering the data was transformed and normalized using variance-stabilizing transformation (VST) and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization.

source_name: Cell line

extract_protocol: mRNA were extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

tag: cell line

tag: growth protocol

value: T47D growing under E2 maintenance

value: basal

tag: batch

tag: description


title: MCF7_LTED_991resistant_batch1_2

value: MCF7-LTED, resistant to estrogen deprivation, treated with Palbociclib (CDK4/6 inhibitor) until became Palbociclib-resistant

value: Palbociclib-resistant

value: replicate 2


title: T47D_WT_basal_batch1_2


title: MCF7_LTED_991resistant_batch1_1

value: replicate 1


title: MCF7_LTED_basal_batch1_3

value: MCF7-LTED, resistant to estrogen deprivation

value: replicate 3


title: MCF7_LTED_basal_batch1_1


title: splenic macrophage Control replicate 1

description:
replicate 1
Sample 1

tag: treatment


title: T47D_WT_991resistant_batch1_1

value: T47D in E2 treated with Palbociclib (CDK4/6 inhibitor) until resistant


title: T47D_WT_991resistant_batch1_3


title: T47D_WT_basal_batch1_1


title: MCF7_WT_991resistant_batch2_2

value: MCF7 in E2 treated with Palbociclib (CDK4/6 inhibitor) until resistant


title: MCF7_LTED_991resistant_batch1_3


title: splenic macrophage Infection 1 replicate 3

description:
replicate 3
Sample 8

value: Mtb UT127

value: Infection 1


title: splenic macrophage Control replicate 4

description:
replicate 4
Sample 10


title: splenic macrophage Control replicate 3

description:
replicate 3
Sample 7


title: splenic macrophage Infection 2 replicate 2

description:
replicate 2
Sample 6

value: Mtb UT205

value: Infection 2


title: MCF7_WT_basal_batch2_3

value: MCF7 growing under E2 maintenance


title: MCF7_LTED_basal_batch1_2


title: T47D_WT_991resistant_batch1_2


title: splenic macrophage Infection 2 replicate 1

description:
replicate 1
Sample 3

value: spleen slices from deceased donor


title: E1910N [miRNA]

description: control

data_processing:
RQ Manager integrated in software from ABI was used to normalize the entire signal generated. Expression level (as fold change) was calculated when both tumor and normal samples had signals in the assays using DataAssist software v2.0 (Life Technologies, http://www.lifetechnologies.com/about-life-technologies.html).  Signals for miRNA that showed either in tumor only or normal only were dropped from analysis.  Fold change was calculated using the 2 -ΔΔCT method.
In the present study, the data are presented as fold change in the target gene expression in tumors normalized to the internal control gene (MammU6) and relative to the normal tissue control (matched normal as calibrator).  Results of the real-time PCR data are represented as CT values, with CT defined as the threshold cycle number of PCRs at which amplified product was first detected.  The average CT was calculated for both the target gene and MammU6 and the ΔCT was determined as (the mean of up to three CT values for the target gene) minus (the mean of the CT values for U6).  The ΔΔCT represented the difference between the paired tissue samples, as calculated by the formula ΔΔCT = (ΔCT of tumor - ΔCT of normal).  The N-fold differential expression in the target gene of a tumor sample compared to its normal sample counterpart was expressed as 2 -ΔΔCT.  For each case, the frequency of dysregulated miRNAs was calculated as the number of dysregulated miRNAs divided by the total number of miRNAs that showed signals in both tumor and normal.  The criteria used to call an miRNA dysregulated were fold changes ≥ 2 or ≤ 0.5.

label: FAM

source_name: normal esophageal epithelia cells

label_protocol: As per manufacturer (ABI).

extract_protocol: Total RNA was extracted and purified by standard Trizol method and using the Allprep Kit (Qiagen). All RNA  quality and quantity were determined using RNA6000 labchip/Agilent 2100 bioanalyzer.

value: normal esophageal epithelia cells

tag: tissue type

value: frozen normal tissue


title: E1910T [miRNA]

description: test

source_name: esophageal squamous cell carcinoma

value: esophageal squamous cell carcinoma

value: frozen tumor tissue


title: E2644T [miRNA]

description: test


title: E1901T [miRNA]

description: test


title: MCF7_WT_991resistant_batch2_3

value: Palbociclib-resistant


title: MCF7_WT_basal_batch2_1

value: basal


title: MCF7_WT_991resistant_batch1_1

value: replicate 1


title: MCF7_WT_991resistant_batch1_3


title: MCF7_WT_basal_batch2_2

value: replicate 2


title: E1892N [miRNA]

description: control


title: E1905T [miRNA]

description: test


title: E1905N [miRNA]

description: control


title: MCF7_WT_991resistant_batch1_2


title: E1902T [miRNA]

description: test


title: E2644N [miRNA]

description: control


title: E1902N [miRNA]

description: control


title: MCF7_WT_basal_batch1_2


title: E1885N [miRNA]

description: control


title: E1880N [miRNA]

description: control


title: E1880T [miRNA]

description: test


title: E1882N [miRNA]

description: control


title: E1885T [miRNA]

description: test


title: E1897N [miRNA]

description: control


title: MCF7_WT_991resistant_batch2_1


title: E1892T [miRNA]

description: test


title: E1882T [miRNA]

description: test


title: E1901N [miRNA]

description: control


title: E1879N [miRNA]

description: control


title: E1879T [miRNA]

description: test


title: E1875N [miRNA]

description: control


title: E1864N [miRNA]

description: control


title: E1874T [miRNA]

description: test


title: E1874N [miRNA]

description: control


title: E1877T [miRNA]

description: test


title: E1864T [miRNA]

description: test


title: E1866N [miRNA]

description: control


title: E1866T [miRNA]

description: test


title: E1897T [miRNA]

description: test


title: E1862T [miRNA]

description: test


title: E1862N [miRNA]

description: control


title: E1875T [miRNA]

description: test


title: MCF7_WT_basal_batch1_1


title: E1860T [miRNA]

description: test


title: E1877N [miRNA]

description: control


title: E1793N [miRNA]

description: control


title: E1796N [miRNA]

description: control


title: E1796T [miRNA]

description: test


title: E1756N [miRNA]

description: control


title: E1793T [miRNA]

description: test


title: E1782N [miRNA]

description: control


title: E1782T [miRNA]

description: test


title: E1860N [miRNA]

description: control


title: E1709N [miRNA]

description: control


title: E1756T [miRNA]

description: test


title: E1709T [miRNA]

description: test


title: E1629N [miRNA]

description: control


title: E1635N [miRNA]

description: control


title: E1635T [miRNA]

description: test


title: E1633T [miRNA]

description: test


title: E1633N [miRNA]

description: control


title: E1629T [miRNA]

description: test


title: E1627N [miRNA]

description: control


title: E1628T [miRNA]

description: test


title: E1628N [miRNA]

description: control


title: E1610N [miRNA]

description: control


title: E1603T [miRNA]

description: test


title: E1627T [miRNA]

description: test


title: E1610T [miRNA]

description: test


title: E1603N [miRNA]

description: control


title: E1584T [miRNA]

description: test


title: E1589T [miRNA]

description: test


title: E1589N [miRNA]

description: control


title: E1578N [miRNA]

description: control


title: E1584N [miRNA]

description: control


title: E1578T [miRNA]

description: test


title: E1577N [miRNA]

description: control


title: E1577T [miRNA]

description: test


title: E1614N [miRNA]

description: control


title: E1575N [miRNA]

description: control


title: E1614T [miRNA]

description: test


title: E1575T [miRNA]

description: test


title: E1573N [miRNA]

description: control


title: E1573T [miRNA]

description: test


title: E1576T [miRNA]

description: test


title: E1566T [miRNA]

description: test


title: E1558N [miRNA]

description: control


title: E1566N [miRNA]

description: control


title: E1556N [miRNA]

description: control


title: E1556T [miRNA]

description: test


title: E1572N [miRNA]

description: control


title: E1572T [miRNA]

description: test


title: E1558T [miRNA]

description: test


title: E1576N [miRNA]

description: control


title: E1546N [miRNA]

description: control


title: E1551T [miRNA]

description: test


title: E1542T [miRNA]

description: test


title: E1542N [miRNA]

description: control


title: E1532N [miRNA]

description: control


title: E1520N [miRNA]

description: control


title: E1521N [miRNA]

description: control


title: E1551N [miRNA]

description: control


title: E1535T [miRNA]

description: test


title: E1521T [miRNA]

description: test


title: E1517N [miRNA]

description: control


title: E1520T [miRNA]

description: test


title: E1517T [miRNA]

description: test


title: E1510N [miRNA]

description: control


title: E1510T [miRNA]

description: test


title: E1498N [miRNA]

description: control


title: E1507T [miRNA]

description: test


title: E1490T [miRNA]

description: test


title: E1478N [miRNA]

description: control


title: E1498T [miRNA]

description: test


title: E1546T [miRNA]

description: test


title: E1535N [miRNA]

description: control


title: E1532T [miRNA]

description: test


title: E1478T [miRNA]

description: test


title: E1475N [miRNA]

description: control


title: E1475T [miRNA]

description: test


title: E1507N [miRNA]

description: control


title: E1490N [miRNA]

description: control


title: E1450N [miRNA]

description: control


title: E1463T [miRNA]

description: test


title: E1451T [miRNA]

description: test


title: E1447T [miRNA]

description: test


title: E1440N [miRNA]

description: control


title: E1416T [miRNA]

description: test


title: E1415N [miRNA]

description: control


title: E1423T [miRNA]

description: test


title: E1435T [miRNA]

description: test


title: E1463N [miRNA]

description: control


title: E1423N [miRNA]

description: control


title: E1416N [miRNA]

description: control


title: E1435N [miRNA]

description: control


title: E1440T [miRNA]

description: test


title: E1451N [miRNA]

description: control


title: E1447N [miRNA]

description: control


title: E1400T [miRNA]

description: test


title: E1405T [miRNA]

description: test


title: E1408N [miRNA]

description: control


title: E1405N [miRNA]

description: control


title: E1400N [miRNA]

description: control


title: E1408T [miRNA]

description: test


title: E1301N [miRNA]

description: control


title: E1293T [miRNA]

description: test


title: E1270N [miRNA]

description: control


title: E1270T [miRNA]

description: test


title: E1415T [miRNA]

description: test


title: E1242N [miRNA]

description: control


title: E1256T [miRNA]

description: test


title: E1241N [miRNA]

description: control


title: E1187N [miRNA]

description: control


title: E1210T [miRNA]

description: test


title: E1195N [miRNA]

description: control


title: E1195T [miRNA]

description: test


title: E1242T [miRNA]

description: test


title: E1293N [miRNA]

description: control


title: E1241T [miRNA]

description: test


title: E1301T [miRNA]

description: test


title: E1187T [miRNA]

description: test


title: E1179N [miRNA]

description: control


title: E1179T [miRNA]

description: test


title: E1450T [miRNA]

description: test


title: E1250N [miRNA]

description: control


title: E1256N [miRNA]

description: control


title: E1164N [miRNA]

description: control


title: E1164T [miRNA]

description: test


title: E1163N [miRNA]

description: control


title: E0978N [miRNA]

description: control


title: E0973T [miRNA]

description: test


title: E0978T [miRNA]

description: test


title: E0973N [miRNA]

description: control


title: E1210N [miRNA]

description: control


title: E0972N [miRNA]

description: control


title: E0945T [miRNA]

description: test


title: E0948T [miRNA]

description: test


title: E0948N [miRNA]

description: control


title: E0945N [miRNA]

description: control


title: E0972T [miRNA]

description: test


title: E1250T [miRNA]

description: test


title: E1163T [miRNA]

description: test


title: E0939N [miRNA]

description: control


title: E0942T [miRNA]

description: test


title: E0942N [miRNA]

description: control


title: E0925T [miRNA]

description: test


title: E0921N [miRNA]

description: control


title: E0939T [miRNA]

description: test


title: E0941N [miRNA]

description: control


title: E0925N [miRNA]

description: control


title: E0941T [miRNA]

description: test


title: E0921T [miRNA]

description: test


title: E0892T [miRNA]

description: test


title: E0891N [miRNA]

description: control


title: E0915N [miRNA]

description: control


title: E0892N [miRNA]

description: control


title: E0891T [miRNA]

description: test


title: E0887N [miRNA]

description: control


title: E0868N [miRNA]

description: control


title: E0864N [miRNA]

description: control


title: E0887T [miRNA]

description: test


title: E0868T [miRNA]

description: test


title: E0864T [miRNA]

description: test


title: E0863N [miRNA]

description: control


title: E0915T [miRNA]

description: test


title: E0863T [miRNA]

description: test


title: E0844N [miRNA]

description: control


title: E0848T [miRNA]

description: test


title: E0848N [miRNA]

description: control


title: E0844T [miRNA]

description: test


title: E0822N [miRNA]

description: control


title: E0842T [miRNA]

description: test


title: E0822T [miRNA]

description: test


title: E0781T [miRNA]

description: test


title: E0781N [miRNA]

description: control


title: E0796N [miRNA]

description: control


title: E0809N [miRNA]

description: control


title: E0742N [miRNA]

description: control


title: E0809T [miRNA]

description: test


title: E0796T [miRNA]

description: test


title: E0782T [miRNA]

description: test


title: E0746N [miRNA]

description: control


title: E0782N [miRNA]

description: control


title: E0746T [miRNA]

description: test


title: E0742T [miRNA]

description: test


title: E0410T [miRNA]

description: test


title: E0842N [miRNA]

description: control


title: E0387T [miRNA]

description: test


title: E0387N [miRNA]

description: control


title: E0381N [miRNA]

description: control


title: E0381T [miRNA]

description: test


title: E0362N [miRNA]

description: control


title: E0379N [miRNA]

description: control


title: E0379T [miRNA]

description: test


title: E0410N [miRNA]

description: control


title: E0362T [miRNA]

description: test