title: Mouse Female 12 weeks

status: Public on May 01 2022

city: Zhunan, Miaoli County

first: Ben-Yang

last: Liao

address: 35 Keyan Rd.

department: Institute of Population Health Sciences

institute: National Health Research Institutes

data_processing:
Illumina Real Time Analysis 3 (RTA3) software was used for basecalling
The bases with low quality and sequences from adapters in raw data were removed using program fastp (v.0.22.0)
Cleaned paired-end reads of FASTQ files derived from various tissue samples were analyzed using kallisto (v.0.46.1)
The kallisto index was built with default parameters from the reference transcriptome file for quantification in each organism.
kallisto computed the transcript abundances as TPMs (Transcripts Per Kilobase Million). The TPM value of the longest transcript was assigned to each gene.
genome build: GRCm39
genome build: mArvNil1.pat.X
processed data files format and content: tab-delimited text files include Ensembl Gene ID and normalized TPM values for each sample.

source_name: Olfactory epithelium

extract_protocol:
The olfactory epithelium was dissected out from the nasal cavity for each sample. The total RNA was isolated by TRIzol Reagent and subsequently purified with the RNeasy Mini Kit (Qiagen, Hilden, Germany). The quantity and purity of the isolated RNA were measured by NanoDrop ND-1000 Spectrophotometer before cDNA library construction.
The cDNA libearies were constructed by TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA). Briefly, mRNA was purified from total RNA (1 μg) by oligo(dT)-coupled magnetic beads and fragmented into small pieces under elevated temperature. The first-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of double-strand cDNA and adenylation on 3’ ends of DNA fragments, the adaptors were ligated, and the samples were purified with AMPure XP system (Beckman Coulter, Beverly, USA). The quality of the libraries was assessed on the Agilent Bioanalyzer 2100 system and a Real-Time PCR system.

tag: tissue

value: olfactory epithelium

value: female

tag: age

value: 12 weeks


title: Mouse Male 16 weeks

type: SRA

country: Taiwan

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: Sex

value: male

value: 16 weeks


title: Nile rat Male 8 weeks

organism: Arvicanthis niloticus

value: 8 weeks


title: Peripheral T cells of patinet #25 before TTF treatment

status: Public on Apr 20 2022

city: SOUTH PASADENA

first: SON

middle: B

last: LE

state: CA

address: 1645 Amberwood Drive, Unit 11

country: USA

institute: University of Southern California

data_processing:
Paired-end reads were trimmed with trimmomatic v/0.36.
Alignment and gene counts were generated against the GRCh38.p12 genome assembly using the annotation GeneCode release 28 by STAR v2.6.0b with default options and quantmode=GeneCounts. Gene expressions in  transcripts per million (tpm)  were calculated as described in  Wagner et all, Theory Biosci. (2012) 131:281–285
the pair end reads from bulk non-targeted RNA-seq were supplied to MiXCR v.3.0.13, using the command analyze shotgun with the option of starting-material rna, only-productive.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample in count or tpm unit and in Ensemble ID and Official gene name
Supplementary_files_format_and_content: Tab delimited format MixCR clonotype fraction file for  each of (ALL, IGH, IGK, IGL, TRA, TRB, TRD, TRG) and each sample

organism: Homo sapiens

source_name: Peripheral T lymphocytes isolated from PBMC

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from blood by density gradient centrifugation (Ficoll-Hypaque) and cryopreserved at liquid nitrogen until processed.

extract_protocol:
Frozen PBMC samples were quickly taken from liquid nitrogen and thaw at 37 degree. T lymphcytes were isolated using Pan T Cell Isolation Kit, human (Miltenyi Cat#130-096-535), and the total RNA was extracted using Qiagen RNA extraction kit.
RNA-seq library performed at ICBR Gene Expression & Genotyping (RRID:SCR_019145) using 25 ng of protein-free, DNase-treated total RNA (each sample processed individually) as input. Briefly, 25ng of total RNA was used for mRNA isolation using NEBNext Ploy(A) mRNA Magnetic Isolation module (New England Biolabs, catalog # E7490 ). Then followed by RNA library construction with NEBNext Ultra II Directional Lib Prep (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Briefly, RNA is fragmented in NEBNext First Strand Synthesis Buffer by heating at 94 °C for desired time. This step is followed by first strand cDNA synthesis using reverse transcriptase and oligo dT primers.  Synthesis of ds cDNA is performed using the 2nd strand master mix provided in the kit, followed by end-repair and adaptor ligation. Finally, library is enriched (each library has an unique barcode) by 12 cycles of amplification, and purified by Agencourt AMPure beads (Beckman Coulter, catalog # A63881).

treatment_protocol: Blood was draw before and one month after TTField treatment started

tag: sample id

tag: treatment

value: untreated

tag: disease

value: Glioblastoma


title: Peripheral T cells of patinet #24 after TTF treatment

value: TTFields


title: Peripheral T cells of patinet #28 after TTF treatment


title: Mouse Male 8 weeks


title: Peripheral T cells of patinet #24 before TTF treatment


title: Peripheral T cells of patinet #22 after TTF treatment


title: Peripheral T cells of patinet #23 after TTF treatment


title: Peripheral T cells of patinet #22 before TTF treatment


title: Peripheral T cells of patinet #23 before TTF treatment


title: IGF106025

status: Public on May 08 2022

city: London

first: Rahel

last: Feleke

address: Ducane Road

country: United Kingdom

institute: Imperial College

data_processing:
Quality control (QC) of RNA-seq reads was conducted using FastQC. Low quality reads and ribosome RNA reads were removed. Trimmed reads were then mapped to the Rattus norvegicus reference genome (rno6) using STAR (version 2.5).
Assembly: Rattus norvegicus genome assembly Rnor_6.0 (rn6)  (Ensembl release 104)
Supplementary files format and content: Raw count matrix

organism: Rattus norvegicus

extract_protocol:
The mRNA Isolation Kit was used to extract total RNA from brain tissue samples following the manufacturer’s instructions.
Total RNA was examined for quantity and quality using the TruSeq Stranded Total RNA Library Prep Gold.

value: Brain

value: NEC

value: non Exposed


title: Peripheral T cells of patinet #19 after TTF treatment


title: IGF106040

value: VPA Exposed


title: Mouse Female 16 weeks


title: Peripheral T cells of patinet #19 before TTF treatment


title: Mouse Male 12 weeks


title: Peripheral T cells of patinet #18 before TTF treatment


title: Peripheral T cells of patinet #25 after TTF treatment


title: Peripheral T cells of patinet #18 after TTF treatment


title: Peripheral T cells of patinet #16 after TTF treatment


title: Peripheral T cells of patinet #16 before TTF treatment


title: Peripheral T cells of patinet #12 after TTF treatment


title: Peripheral T cells of patinet #12 before TTF treatment


title: Peripheral T cells of patinet #14 before TTF treatment


title: Peripheral T cells of patinet #14 after TTF treatment


title: Peripheral T cells of patinet #9 after TTF treatment


title: Peripheral T cells of patinet #7 after TTF treatment


title: IGF106037


title: Peripheral T cells of patinet #7 before TTF treatment


title: CONTROL11

status: Public on Mar 22 2022

city: Boston

first: Jonathan

middle: David

last: Lee

state: MA

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

data_processing:
Raw sequencing reads were aligned to a reference transcriptome generated from the Ensembl v104 human transcriptome with salmon v1.4.0 using options “--seqBias --useVBOpt --gcBias --posBias --numBootstraps 30 --validateMappings”.
Genome_build: hg38
Supplementary_files_format_and_content: .sf.txt files from salmon v1.4.0. The columns represent the following:  Name: the name of the target transcript provided in the input transcript database (FASTA file).  Length: the length of the target transcript in nucleotides.  EffectiveLength: the computed effective length of the target transcript.  TPM: the estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM).  NumReads: the estimate of the number of reads mapping to each transcript that was quantified.

source_name: Frontal cortex of brain

extract_protocol:
Frozen tissue was processed using Biosafety Level 2+ (BL2+) procedures approved by the Beth Israel Deaconess Medical Center (BIDMC) Institutional Biosafety Committee (IBC). Brain tissues and primary neurons were homogenized using Trizol (Thermo Fisher) reagent and RNA extracted by phase separation. Total RNA was quantified by nanodrop (DeNovix DS-11) and TapeStation 4200 (RNA Screen Tape; Agilent Technologies, Inc).
450 ng of total RNA was used for library preparation via the KAPA RNA HyperPrep kit with RiboErase (HMR; Roche) according to the manufacturer’s recommendations. Briefly, hybridization with hybridization oligos (HMR) was performed at 95oC for 2min followed by rRNA depletion using RNAse H which was performed at 45 oC for 30min. Following rRNA cleanup via KAPA pure beads, DNase digestion was performed at 37 oC for 30min followed by cleanup, RNA elution, fragmentation (6 min at 94oC for samples with RIN ≥ 7 or 5min at 85 oC for samples with RIN ≤ 7) and priming. First and second strand synthesis and A-tailing were performed according to manufacturer’s recommendations. 1.5 uM KAPA Unique Dual-Indexed (UDI; Roche) adapters were ligated to the second strand synthesis product in the presence of a ligation master mix in a reaction that was performed at 20 oC for 15min. Following cleanup, all libraries underwent 10 cycles of amplification. Successful library production, quality control, and quantification was assessed using Tapestation (High sensitivity D1000 Screen Tape; Agilent Technologies, Inc). Libraries were pooled and sequenced via NovaSeq 6000.

value: Frontal cortex of brain

value: F

tag: matching group

value: H

tag: group

value: Control


title: scRNA_Trim28_E6.5

status: Public on Mar 30 2022

city: Berlin

first: Sara

last: Hetzel

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: Single-cell RNA-sequencing of Trim28 knock-out E6.5 mouse embryos

data_processing:
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Single-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, version 4.0.0, default parameters).
For each experiment FASTQ files were aligned, filtered, barcode and UMI counted using 10X Genomics' Single-Cell Gene Expression Software Cell Ranger ("count pipeline", version 4.0.0, default parameters). The count pipeline was run jointly on multiple sequencing runs of the same experiment. Genomic reference as prepared by 10x Genomics.
For experiments with multiple libraries, all libraries were aggregated using 10X Genomics' Single-Cell Gene Expression Software Cell Ranger ("aggr pipeline", version 4.0.0, default parameters). The output of Cell Ranger "count" was aggregated and normalized to the same sequencing depth and then the gene-barcode matrices were recomputed on the combined data. Sample aggregation was evaluated with normalizing for sequencing depth differences in the libraries. Normalized UMI counts used the 'mapped' normalization mode. Analysis of the data was based on the normalized UMI counts.
Genome_build: mm10
For all samples there is one tar gz archive containing the raw gene-barcode matrices as produced by the Cell Ranger pipeline. They contain the MEX-formatted UMI count matrices of each sample, or if multiple libraries where sequence, the aggregated gene-barcode matrix. 10x Genomics explains their MEX-formatted UMI counts as follows: "The cellranger pipeline generates a gene-barcode matrix... Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively." More information on the formatting can be found at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices.

molecule: polyA RNA

source_name: E6.5 embryonic and extraembryonic tissues

growth_protocol: Preimplantation embryos were cultured in pre-gassed 25 ul KSOM supplemented with 1/2 amino acids (Millipore) under mineral oil at 37ºC and 5% CO2.  After ~84 hours post-fertilization, cavitated blastocysts were transferred into the uterine horns of pseudopregnant females in clutches of 10-15 per horn.

extract_protocol:
Respective gene null (KO) embryos were isolated from surrogate mice. Outermost extraembryonic tissues (yolk sac, trophectoderm derived tissues) were preserved if possible. The 7-11 embryos isolated per experiment were washed in 1xPBS/0.4%BSA, pooled without pre-selection and subjected to tissue dissociation in 200 µl TrypLE Express (Gibco) for 40-60 minutes at 37ºC, with pipetting in 5 minute intervals. The cell suspension was filtered using Scienceware Flowmi Cell Strainers, 40 µM. Cells were washed twice with 1ml 1xPBS/0.4%BSA and centrifugation for 5 minutes at 1200 rpm. The cell concentration was determined using a hemocytometer and cells were subjected to single-cell RNA sequencing (10x Genomic, Chromium™ Single Cell 3’ v2).
Single-cell libraries were generated following the manual instructions of 10x Genomic (Chromium™ Single Cell 3’ v2 or v3), with the exception of fewer PCR cycles in cDNA amplification and sample index PCR than recommended in order to increase complexity of libraries. Libraries were sequenced with a minimum of 230 Mio paired end reads and parameters as described in the manual.

treatment_protocol: B6D2F1 oocytes were isolated from 5-10 week old female mice ~12h after a hormone priming superovulation regime (5 IU PSMG and 5IU hCG delivered 46 hours afterwards) and stored in 25 ul droplets of pregassed KSOM media with 1/2 amino acids (Millipore) at 37ºC and 5%C02 .  Zygotes were generated either by intracytoplasmic sperm injection of decapitated B6/CAST F1 strain sperm (RNA-seq) or natural mating with B6D2F1 males (Bisulfite-seq) and cultured to E3.5 blastoycsts prior to uterine transfer into pseudopregnant CD-1 strain females (~25-35 g).  Post-implantation embryos were isolated according to the embryonic day with a 24 hour offset to accommodate developmental delay as a result of uterine transfer (see extract protocol).  Experimental samples were additionally injected with a cocktail of 3-4 discrete gRNA's targeted to exons of respective KO gene and Cas9 mRNA synthesized by in vitro transcription at concentrations of 33.3 ng/ul per gRNA and 200 ng/ul for Cas9.  gRNA/Cas9 injections occurred within 6-8 hours post fertilization, followed by equivalent culture in KSOM media to the blastocyst stage as the control.

tag: cell line

value: B6D2F1 maternal strain crossed with B6/CAST F1 males

value: Trim28 KO


title: CONTROL12

value: M

value: I


title: Peripheral T cells of patinet #9 before TTF treatment


title: scRNA_WT_E5.5

description: Single-cell RNA-sequencing of wild-type E5.5 mouse embryos

source_name: E5.5 embryonic and extraembryonic tissues

treatment_protocol: B6D2F1 oocytes were isolated from 5-10 week old female mice ~12h after a hormone priming superovulation regime (5 IU PSMG and 5IU hCG delivered 46 hours afterwards) and stored in 25 ul droplets of pregassed KSOM media with 1/2 amino acids (Millipore) at 37ºC and 5%C02 .  Zygotes were generated by in vitro fertilization (IVF) with  B6/CAST F1 strain sperm. Zygotes were electroporated with Cas9-RNP  with guides targeting GFP as non-target or mock using NEPA21 electroporator; and allowed to develop until E3.5 blastocyst stage prior to uterine transfer into pseudopregnant CD-1 strain females (~25-35 g).  Post-implantation embryos were isolated according to the embryonic day with a 24 hour offset to accommodate developmental delay as a result of uterine transfer (see extract protocol).

value: wild-type


title: CONTROL7

value: D


title: CONTROL9


title: CONTROL8

value: E


title: CONTROL6


title: CONTROL5

value: C


title: CONTROL10

value: G


title: CONTROL2

value: B


title: CONTROL4


title: CONTROL1

value: A


title: COVID11


title: COVID12


title: COVID10


title: CONTROL3


title: Myotube_Healthy_Subject4

status: Public on Apr 19 2022

type: RNA

city: Londonderry

first: William

middle: John

last: Duddy

address: C-TRIC building, Altnagelvin Hospital Campus

department: Northern Ireland Centre for Stratified Medicine

institute: Ulster University

description: Healthy subject, primary myoblasts extracted from deltoid muscles and differentiated for 3 days to form myotubes

hyb_protocol: Following fragmentation and end-labeling, 4.7 μg of cDNAs were hybridized for 16 hours at 45oC. The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: Raw data (.CEL Intensity files) were processed using R/Bioconductor packages. Briefly, sample quality was verified by assessment of MA plots, normalized unscaled standard error (NUSE; all samples had median <1.1), and relative log expression (RLE; all sample had divergence <0.2), using the oligo package. Background-corrected normalized log2-transformed probe set signal intensities were obtained by Robust Multi-array Averaging (RMA) using default settings. Affycoretools and huex10stprobeset.db were used to annotate probeset IDs. For exon-level analysis, probesets were retained if oligo’s paCalls function declared them present with p<0.05 in all samples of at least one experimental group. For gene-level analysis, probesets were retained if they had expression level >log250 in at least 4 of the 23 samples. After filtering, expression matrices were written to file in tab-delimited format.

label: biotin

source_name: Myotubes of Healthy subject

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 150 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations.

growth_protocol: Muscle samples were obtained by open biopsy of deltoid muscle. Muscles biopsies were dissociated mechanically and plated in proliferation medium. The myogenic cell population was enriched using a CD56 magnetic bead and for their myogenicity using anti-desmin antibodies. A minimum of 80% of the cell population were positive for desmin. After rinsing 3 times the proliferative myoblasts with PBS, and 3 times with DMEM to remove any FBS residual, the human muscle stem cells were differentiated into myotubes by culturing them in DMEM for 3 days.

extract_protocol: Purified muscle stem cells were differentiated for 3 days into myotubes. Total RNA from muscle cells was extracted.  The quality of RNA samples was assessed with Agilent 2100 Bioanalyzer.

tag: pathology

value: Healthy

tag: age (years)

tag: gender

value: Male

tag: source muscle

value: Deltoid

tag: cell type

value: myotubes


title: Myotube_Healthy_Subject5


title: Myotube_ALS_Subject6

description: ALS subject, primary myoblasts extracted from deltoid muscles and differentiated for 3 days to form myotubes

source_name: Myotubes of ALS subject

value: ALS


title: Myotube_Healthy_Subject6


title: Myotube_ALS_Subject3


title: Myotube_Healthy_Subject3


title: Myotube_Healthy_Subject2


title: Myotube_ALS_Subject2


title: Myotube_ALS_Subject5


title: Myotube_ALS_Subject4


title: Myotube_Healthy_Subject1


title: Myotube_ALS_Subject1


title: Pulmonary endothelial cells - ECOLA_SI_3 RNA-seq

status: Public on Jan 14 2022

city: Milwaukee

first: Adeleye

middle: J.

last: Afolayan

state: Wisconsin

address: 8701 Watertown Plank Rd., PD278, CRI TBRC, Rm C3278

institute: Medical College of Wisconsin

data_processing:
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner
Transcript is assembled by StringTie with aligned reads
Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage. The FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) value or the RPKM (Reads Per Kilobase of transcript per Million mapped reads) is used as a normalization value
Genome_build: UCSC hg37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HPAEC cells

growth_protocol: Pulmonary-derived arterial endothelial cells (ATCC) were generated by plating on TC-treated plastic (typically 2–3 × 106 cells into a 100mm dish) with Vasculife EC Media (Lifeline Cell Technology, Frederick, MD, USA).

extract_protocol:
Cells were collected using trypsin and RNA was gathered using the Qiagen RNeasy kit (cat. 74004)
Libraries were prepared according to Lexogen's instruction accompanying the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Cat. 015). Briefly, total RNA was reverse transcribed by oligodT priming, RNA template was removed, and the second strand was synthesized by random priming using DNA polymerase. After bead purification, library is amplified by PCR and sequences required for cluster generation are introduced. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Cells were transfected at ~50% confluency for 24 hours with Fugene 6 transfection reagent (Fugent, Middleton, WI, USA), followed by 24 hours rest.

value: Pulmonary-derived endothelial cells

tag: transfection

value: OLA1 siRNA knockdown


title: COVID5

value: Frontal cortex of brain


title: COVID1

value: M


title: COVID2

value: F


title: Pulmonary endothelial cells - ECOLA_SI_1 RNA-seq


title: COVID4


title: Pulmonary endothelial cells - ECCTRL_2 RNA-seq


title: COVID6


title: Pulmonary endothelial cells - ECOLA_SI_2 RNA-seq


title: COVID7


title: COVID3


title: PBMCs, VSV-LV

status: Public on Oct 01 2021

city: Langen

first: Christian

last: Buchholz

state: Hessen

address: Paul-Ehrlich-Strasse 51-59

institute: Paul Ehrlich Institut

data_processing:
Seven Bridges Bioinformatics Platform(Filtering, Alignment, run locally in a server)
Use default settings of:
template_targeted_1.9-beta.yml (available at https://bitbucket.org/CRSwDev/cwl/src/master/)
rhapsody_targeted_1.9-beta.cwl (available at https://bitbucket.org/CRSwDev/cwl/src/master/)
Genome_build: 1046_vial_gene_masked_amplicons (Derived from GRCh38 plus the usersuppliedsequence = CAR)
Supplementary_files_format_and_content: csv (Metrics Summary output)
Supplementary_files_format_and_content: csv (Gene / cell count matrix)

source_name: PBMC

growth_protocol: RPMI medium with 10% FCS, 2 mM glutamine, 0.5% penicillin/streptomycin, 25 mM HEPES

extract_protocol:
Nanowell-based scRNA isolation and library preparation based on manufacturer's instructions (BD Biosciences) for targeted gene amplification
BD Rhapsody, Immune Response Panel, usersuppliedsequence = CAR
scRNA-seq

treatment_protocol: Cells inoculated with a specified MOI of LVs

tag: time

value: 6 days expansion

value: Conventional LV

tag: moi

value: CAR T cells


title: Pulmonary endothelial cells - ECCTRL_1 RNA-seq


title: 18mo

status: Public on Aug 24 2021

city: Saint Louis

first: Andrea

last: Santeford

state: MO

address: 660 S. Euclid Ave.

department: Opthalmology

institute: Washington University School of Medicine

description:
mRNA
mirSeq_3-30months.txt

data_processing:
For miRNA analysis from RNAseq of 3 to 30 months C57Bl/6 WT samples: Sequencing reads were analyzed using Cofactor Genomics EXP software and aligned to the mouse mm9 genome. Overlapping reads were clustered together to assemble expressed loci and provide respective counts and coverage levels for each loci. Coverage was calculated by $alignedBases/$coveredBases. 6x cutoff of cluster depth corresponding to Integer(sequencedBases/integer(genomeBases)). In order to allow cross sample comparative expression between small-RNAs, all counts and expression levels were normalized to the sample with the fewest reads. A pair-wise comparison was performed between samples and logs2 ratios were computed for each expressed small-RNA.
For RNAseq analysis of macrophages from miR-146b knockout and wildtype littermate controls: Second mate was used for sample demultiplexing. Individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All. Gene expression was obtained via ht-seq and DESeq2 for differential expression. Gene expression was obtained using in-house scripts based on MACS and HTSeq (https://github.com/ctlab/quant3p).
For scRNA-seq: Data was analyzed first using Cellranger 3.1.0 and mapped to the mouse mm10 genome with default parameters. Expression matrices were reanalyzed using Monocle3 (v0.2.1) (44). Initial clustering identified minor contamination (<1%) of cells not expressing macrophage markers (Emr1, Mertk, Csf1r, and Cd68) that were removed from further analyses. tSNE-dimension reduction was performed on the top principal components learned from the 317 genes with the highest variance across the cells that passed quality filters (>5000 mRNA counts) and the Louvain method was used to define clusters. The Monocle3 fit_models() function with the following parameters (model_formula_str = "~library + 1") was used to asses differential gene expression.
Genome_build: For miRNA analysis of C57Bl/6 3-30 month macrophages: mmu9 (MGSCv37)
Genome_build: For RNAseq and single-cell RNAseq analyses of Lys2 Cre+/-; miR146b conditional knockout macrophages and littermate controls: mmu10 (GRCm38)
Supplementary_files_format_and_content: mirSeq_3-30months.txt
Supplementary_files_format_and_content: counts.txt
Supplementary_files_format_and_content: *.tar: Tar archives of barcodes.tsv, features.tsv, and matrix.mtx files.

source_name: peritoneal macrophage

growth_protocol: Macrophages were harvested by peritoneal lavage 4 days post-IP injection with 4% Thioglycollate and plated in DMEM containing 10% FBS, 1% L-glutamine, and 1% Penicillin/Streptomycin. Cells were allowed to adhere to the plate overnight, followed by 3-4 washes in DPBS to remove non-adherent cells. Complete DMEM was replaced and cells were rested for 24hours prior to harvest for RNA isolation.

extract_protocol:
Macrophage mRNA was extracted using MirVana mRNA isolation kit (Life Technologies). >10ug RNA was used to create cDNA libraries.
Poly(A) RNA was isolated to reduce the non-coding (ncRNA) copy number in the pool. The RNA was randomly fragmented and converted to cDNA using standard chemistries for sequencing on the Illumina GAII sequencing platform.

tag: genotype

value: WT

tag: age

value: 18 months

value: Peritoneal macrophage


title: 30mo

description:
mRNA
mirSeq_3-30months.txt

tag: strain

value: 30 months


title: 12mo

description:
mRNA
mirSeq_3-30months.txt

value: 12 months


title: 6mo

description:
mRNA
mirSeq_3-30months.txt

value: 6 months


title: 3mo

description:
mRNA
mirSeq_3-30months.txt

value: 3 months


title: 24mo

description:
mRNA
mirSeq_3-30months.txt

value: 24 months


title: PDC34

status: Public on Aug 15 2021

data_processing:
Sequenced reads were demultiplexed and processed using Cell Ranger (v 3.0.2)
Genome_build: GRCh38 human reference genome (Ensembl v93 gene annotations)
Supplementary_files_format_and_content: Raw count matrix

source_name: Anterior cingulate cortex

extract_protocol:
For each individual, a tissue block of cortical grey matter from the anterior cingulate was sectioned at 80 µm thickness. Adjacent sections were subsequently used for bulk-tissue RNA isolation (2 sections per sample) or isolation of nuclei for single-nuclei RNA-sequencing. Nuclei were isolated using buffers prepared as in Krishnaswami et al., including nuclei isolation medium #1 (NIM1), nuclei isolation medium #2 (NIM2), Homogenisation Buffer (HB), 29% and 50% vol/vol iodixanol dilutions. Briefly, brain tissue sections were suspended in 800 µL HB and homogenised in a pre-cooled 2 mL dounce homogeniser, with five strokes of the loose pestle, followed by 10-15 strokes with the tight pestle. The homogenate was filtered through a BD Falcon tube with a cell strainer cap (35 µm) and centrifuged at 1000 g for 8 minutes. Thereafter, nuclei were subjected to an additional clean-up step (density gradient centrifugation), as detailed in Krishnaswami et al., albeit with centrifugation of the layered nuclei/29% iodixanol solution at 13,000 g for 40 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet washed with PBS buffer (PBS + 1% BSA + 0.2 U/ml RNAseIn), filtered through a BD Falcon tube with a cell strainer cap, centrifuged at 500 g for 5 minutes at 4 °C and washed again. Nuclei were counted using a LUNA-FL Dual Fluorescence Cell Counter (Logos Biosystems, L20001) using Acridine orange dye to stain nuclei.
All samples were processed as per 10X Genomics Chromium Single Cell Reagent Kits Protocol, (chemistry: Single Cell 3' v2). Following manufacturer’s guidelines, the samples were processed to target 10,000 nuclei per sample. Briefly, we performed 8 cycles of cDNA amplification and 14 cycles of final indexing PCR. cDNA concentrations were measured using Qubit dsDNA HS Assay Kit (ThermoFisher, Q32851), and cDNA and library preparations were assessed using the Bioanalyzer High-Sensitivity DNA Kit (Agilent, 5067-4627). All samples were pooled to equimolar concentration and sequenced together across twenty-eight lanes on an Illumina Hi-Seq 4000.
cDNA and library preparations were assessed using the Bioanalyzer High-Sensitivity DNA Kit (Agilent, 5067-4627).

tag: disease state

value: Control

tag: tissue

value: Anterior cingulate cortex

tag: molecule subtype

value: Single-nucleus RNA


title: PDC91


title: Pulmonary endothelial cells - ECCTRL_3 RNA-seq

value: Pulmonary-derived endothelial cells


title: PDC22


title: PDC05


title: PD747

value: PD


title: PBMCs, Untransduced

tag: treatment

value: control


title: PD706

value: DLB


title: PBMCs, CD8-LV

value: 6 days expansion

value: CD8-targeted LV


title: PD732


title: PDC87


title: PD566


title: PD678

value: PDD


title: PD563


title: PD531


title: PD523


title: PD501


title: PD416


title: PD413


title: PD341


title: PD366


title: PD163


title: PD294


title: PD115


title: C48


title: PD060


title: PD683


title: 89_TRIM24 COE

status: Public on Jun 29 2021

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

description:
This is a tumor sample obtained from Cre driven TRIM24 overexpressing mammary gland.
shah.txt
89

data_processing:
Sequences were checked for qulaity of reads using FastQC.
Sequences were aligned to genome assembly mm10 for ucsc using tophat.
Sequences were annotated using ucsc genome annotation and cufflinks.
Annotated gtf files were processed and also converted to transcripts per million using RSEM.
Raw reads were used for post-analysis using R packages DESeq and EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with transcripts per million

source_name: mammary tumor

extract_protocol:
To perform deep sequencing of RNA (RNA-seq), total RNA was isolated from three individual tumors along with five freshly isolated, disease free mammary glands (controls) using size-selection, glass fiber filter-based mirVana RNA isolation kits (Ambion, REF#AM1560, Lot#00310947). Sequencing was performed by the M.D. Anderson Next Generation Sequencing Core Facility. The sequencing data were analyzed using DESeq and edgeR to determine differentially expressed genes (DEGs). The edgeR is also used to perform GSEA and pathway analysis upon TRIM24 over-expression
TruSeq Stranded Total RNA

value: FVB

value: TRIM24 overexpression

tag: subtype

value: Carcinoma

tag: sequencing batch


title: PD666


title: COVID8

value: Frontal cortex of brain

tag: Sex

value: F

tag: matching group

value: E

tag: group


title: C36


title: PD415


title: Patient 9 HNSCC10

status: Public on Mar 09 2021

city: Baltimore

first: Rania

middle: Hassan

last: Younis

state: MD

address: 650 W Batimore St

department: Oncology and Diagnostic Sciences

institute: University of Maryland School of Dentistry

hyb_protocol: Hybridization was carried in a regular thermal cycler. The hybridized mix was purified using magnetic beads in the nCounter machine in the institute of genome sciences (IGS) University of Maryland, Baltimore.

scan_protocol: nCounter digital analyser scan with 555FOVs was used and image acquisition was on the ncounter SPRINT system

data_processing: Data analysis was carried using IO-360 platform 770 genes code sets using the nSolver 4.0 software basic and advanced costumed analysis.

label: Fluorescent

source_name: Head and neck cancer

label_protocol: Biotinylated capture probes and color coded reporter probes were used for the hybridization complex, according to the manufacturer's protocol

extract_protocol:
Three to five slides of 5 um thick FFPE tissue sections of prospectively collected HNSCC tumor tissue were used for RNA extraction using Rneasy FFPE kit (Qiagen, catalog no 73504). The tumor rich areas and 3-4mm of peritumoral stromal were identified and manually micro-dissected by a surgical oral pathologist (RY) guided by H&E stained section.
RNA quality control (QC) analysis was run on nanochip, to ensure required 200nt in 50-300ng with no prior amplification or enzymatic reaction.

value: Head and neck squamous cell carcinoma

tag: gender

value: Female

tag: location

value: Caucasian

tag: race

value: Oral cavity and mobile tongue

tag: Stage

value: IV

tag: soluble sema4d

value: High levels

tag: histological inflammatory subtype sema4 score

value: Immune-desert


title: Patient 8 HNSCC09

tag: age

value: Low levels

value: Immune-excluded / immune-desert


title: Patient 7 HNSCC08

value: Male

value: African American

value: I

value: Immune-excluded


title: Healthy control 3_HC3

status: Public on Jan 06 2021

city: HANGZHOU

first: Qi

last: Cheng

state: Zhejiang

address: 88 Jiefang Road

department: rheumatology

country: China

institute: the Second Affiliated Hospital of Zhejiang University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads. We used Tophat v2.1.0 [1] to map the cleaned reads to the GRCh38 reference genome with two mismatches.
Cufflinks v2.1.1 was run with a reference annotation to generate FPKM values for known gene models. Differentially expressed genes were identified using Cuffdiff.The p-value significance threshold in multiple tests was set by the false discovery rate (FDR) [3,4]. The fold-changes were also estimated according to the FPKM in each sample.The differentially expressed genes were selected using the following filter criteria: FDR ≤0.05 and fold-change ≥2.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM and Reads counts for each Sample

source_name: healthy control

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Cat# 217004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Venous blood samples were get from healthy controls and SLE. Human PBMCs were isolated using a Ficoll method based on the density difference between PBMCs and other components in the blood.

value: healthy control

value: Peripheral Blood

tag: cell type

value: PBMCs


title: Healthy control 4_HC4

tag: disease state


title: SLE patient 5_SLE5

source_name: systemic lupus erythematosus

value: systemic lupus erythematosus

tag: tissue


title: Healthy control 1_HC1


title: Patient 3 HNSCC04

value: Head and neck squamous cell carcinoma

value: Inflammed


title: Healthy control 2_HC2


title: SLE patient 3_SLE3


title: Patient 5 HNSCC06

value: Female

value: Caucasian

value: II


title: SLE patient 4_SLE4


title: SLE patient 1_SLE1


title: Patient 1 HNSCC01

value: Oral cavity and mobile tongue

value: High levels


title: Patient 4 HNSCC05

value: Low levels


title: Patient 2 HNSCC03

value: IV


title: SLE patient 2_SLE2


title: PD332

value: DLB

value: Anterior cingulate cortex

tag: molecule subtype

value: Single-nucleus RNA


title: Healthy control 5_HC5


title: Rec12-201-6xHis-2xFLAG ChIP in pat1-114, rad50S, GFP-Pir1-SD cells

status: Public on Dec 22 2020

type: genomic

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description: ChIP was performed using anti-FLAG-agarose (A2220) followed by microarray analysis

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 or ChIP-v1_10_Apr08 protocol). Signal was normalized by combined rank consistency filtering with LOWESS intensity normalization.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: immunoprecipitated Rc12-DNA linkages

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: For H3K9me2 and Pir1 ChIP, standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Cultures were grown at 30˚C. For Rec12-DNA linkages ChIP, pat1-114 cells were nitrogen starved with EMM-N at 26˚C for 6 h to arrest the cells in G1. The starved cultures were centrifuged and resuspended in EMM medium in 34˚C to induce synchronized meiosis for 4.5 h.

extract_protocol: Cells were lysed with glass-beads, DNA sheared by sonication to 400-600bp fragments and immunoprecipitated with H3K9me2 antibody (Abcam, ab1220), c-MYC antibody (Biolegend, 9E10), or GFP antibody (Abcam, ab290). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C. The Rec12-DNA linkages were recovered by incubation with anti-FLAG-agarose (A2220).

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 30˚C. For GFP and c-MYC ChIPs, fixed cultures were subjected to additional crosslinking with 10 mM DMA for 45 min at room temperature. For Rec12-DNA linkages ChIPs, induced meiotic cells  were collected without paraformaldehyde or DMA treatment.

tag: growth temperature

value: cells growing in 34˚C

tag: genotype

value: pat1-114 rad50S cells expressing GFP-Pir1-SD and Rec12-201-6xHis-2xFLAG

source_name: Whole-cell extract DNA


title: RNA sequencing of WT cells 3

data_processing:
Reads were quality trimmed using Trimmomatic and aligned to the Pombase v2.29 reference genome (Wood et al. 2003) using the STAR (Dobin et al. 2013) aligner and normalized to reads per million (RPM).  Aligned reads were assigned to transcripts on the basis of Pombase annotations using Rsubread. DEGseq (Wang and Wang 2018) was used to compute the log2 fold-change in transcript expression between experimental strains and previously published WT grown at 30°C (Gallagher et al. 2018). Data for WT grown at 30°C can be found at GEO Omnibus accession numbers GSM2803075 and GSM2803077.
Genome_build: Pombase Schizosaccharomyces pombe asm294v2.29
Supplementary_files_format_and_content: Feature count tables from DEGseq; feature counts and bedgraphs generated by STAR and post-processed to produce uniform sampling intervals.

source_name: cells growing in EMM at 29˚C

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Logarithmically growing pat1-as2 cells were starved in nitrogen depletion media (EMM-N) for 4-7h, then treated with 25 µM 1-NM-PP1 to triger meiosis.

extract_protocol:
RNA was extracted using MasterPure Yeast RNA purification kit (MPY03100, Lucigen) according to manufacturer's recommendation.
ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre) or Ultra II Directional RNA Library Prep Kit for Illumina (NEB) was used according to manufacturer's recommendation.
Libraries were analyzed using an Agilent 2100 BioAnalyzer (Agilent) and sequenced on the Illumina MiSeq Platform or Illumina NextSeq 500 platform.

value: wild type mat1Msmt0 cells


title: RNA sequencing of pir1∆ cells 2

source_name: cells growing in YEA at 29˚C

value: pir1-delta mat1Msmt0 cells


title: GFP-Pir1-SD ChIP in tor2ts cells

description: ChIP was performed using anti-GFP antibody (ab290) followed by microarray analysis

source_name: GFP-Pir1-SD immunoprecipitated DNA

value: cells growing in 30˚C

value: tor2ts cells expressing GFP-Pir1-SD


title: RNA sequencing of pir1∆ cells 3


title: GFP-Pir1-SA ChIP in tor2ts cells

source_name: GFP-Pir1-SA immunoprecipitated DNA

value: tor2ts cells expressing GFP-Pir1-SA


title: H3K9me2 ChIP in tor2ts GFP-Pir1-SA cells

description: ChIP was performed using anti-H3K9me2 antibody (ab1220) followed by microarray analysis

source_name: H3K9me2 immunoprecipitated DNA

value: tor2ts GFP-Pir1-SA cells


title: RNA sequencing of WT pir1-SA cells

source_name: cells growing in EMM at 18˚C

value: wild type h90 cells expressing GFP-Pir1-SA


title: RNA sequencing of WT pir1-SD cells

value: wild type h90 cells expressing GFP-Pir1-SD


title: Rec12-201-6xHis-2xFLAG ChIP in pat1-114, rad50S, GFP-Pir1 cells

value: pat1-114 rad50S cells expressing GFP-Pir1 and Rec12-201-6xHis-2xFLAG


title: H3K9me2 ChIP in tor2ts ubi4D cells

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 or ChIP-v1_10_Apr08 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

source_name: H3K9me2 ChIP_tor2ts ubi4D

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Cultures were grown at 30˚C.

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 400-600bp fragments and immunoprecipitated with H3K9me2 antibody (Abcam, ab1220), c-MYC antibody (Biolegend, 9E10),  or GFP antibody (Abcam, ab290). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 25˚C. For GFP and c-MYC ChIPs, fixed cultures were subjected to additional crosslinking with 10 mM DMA for 45 min at room temperature.

value: cells growing in 30C

value: tor2ts ubi4D cells


title: Pir1-MYC ChIP in WT cells

description: ChIP was performed using anti-c-MYC antibody (9E10) followed by microarray analysis

source_name: Pir1-MYC ChIP_WT

value: WT cells expressing Pir1-MYC


title: Pir1-MYC ChIP in tor2ts cul4D cells

source_name: Pir1-MYC ChIP_tor2ts cul4D

value: tor2ts cul4D cells expressing Pir1-MYC


title: H3K9me2 ChIP in tor2ts ddb1D cells

source_name: H3K9me2 ChIP_tor2ts ddb1D

value: tor2ts ddb1D cells


title: H3K9me2 ChIP in WT cells

source_name: H3K9me2 ChIP_WT

value: Wild type cells


title: RNA sequencing of WT pir1-WT cells 3

value: wild type h90 cells expressing GFP-Pir1


title: H3K9me2 ChIP in tor2ts GFP-Pir1-SD  cells

value: tor2ts GFP-Pir1-SD cells


title: Pir1-MYC ChIP in tor2ts cells

source_name: Pir1-MYC ChIP_tor2ts

value: tor2ts cells expressing Pir1-MYC


title: H3K9me2 ChIP in pir1D cells

source_name: H3K9me2 ChIP_pir1D

value: pir1D cells


title: H3K9me2 ChIP in nitrogen repletion treated WT cells

source_name: H3K9me2 ChIP_+nitrogen


title: H3K9me2 ChIP in 0.1% Glucose treated WT cells

source_name: H3K9me2 ChIP_0.1% Glucose


title: H3K9me2 ChIP in tor2ts cells

source_name: H3K9me2 ChIP_tor2ts

value: tor2ts cells


title: H3K9me2 ChIP in 0.5% Glucose treated WT cells

source_name: H3K9me2 ChIP_0.5% Glucose

source_name: Whole-cell extract DNA


title: GFP-Pir1 ChIP in WT cells

source_name: GFP-Pir1 ChIP_WT

value: WT cells expressing GFP-Pir1


title: Pir1-MYC ChIP in tor2ts ubi4D cells

source_name: Pir1-MYC ChIP_tor2ts ubi4D

value: tor2ts ubi4D cells expressing Pir1-MYC


title: GFP-Pir1 ChIP in tor2ts cells

source_name: GFP-Pir1 ChIP_tor2ts

value: tor2ts cells expressing GFP-Pir1


title: H3K9me2 ChIP in 2% Glucose treated WT cells

source_name: H3K9me2 ChIP_2% Glucose


title: H3K9me2 ChIP in nitrogen starvation treated WT cells

source_name: H3K9me2 ChIP_-nitrogen


title: H3K9me2 ChIP in tor2ts GFP-Pir1 cells

source_name: H3K9me2 immunoprecipitated DNA

value: cells growing in 30˚C

value: tor2ts GFP-Pir1 cells


title: RNA sequencing of red1∆ pat1-as2 diploid cells_26C_7h

source_name: cells growing in EMM with 25µM 1-NM-PP1 at 26˚C for 7h

tag: strain

value: red1_delta pat1-as2 diploid cells


title: RNA sequencing of red1∆ pat1-as2 diploid cells_26C_8h

source_name: cells growing in EMM with 25µM 1-NM-PP1 at 26˚C for 8h


title: RNA sequencing of pir1∆ pat1-as2 diploid cells_26C_8h

value: pir1_delta pat1-as2 diploid cells


title: RNA sequencing of pir1∆ pat1-as2 diploid cells_26C_7h


title: RNA sequencing of pir1∆ pat1-as2 diploid cells_26C_5h

source_name: cells growing in EMM with 25µM 1-NM-PP1 at 26˚C for 5h


title: RNA sequencing of pir1∆ pat1-as2 diploid cells_26C_6h

source_name: cells growing in EMM with 25µM 1-NM-PP1 at 26˚C for 6h


title: RNA sequencing of pir1∆ pat1-as2 diploid cells_26C_4h_EMM-N

source_name: cells growing in EMM-N at 26˚C for 4h


title: RNA sequencing of pir1∆ pat1-as2 diploid cells_26C_3h

source_name: cells growing in EMM with 25µM 1-NM-PP1 at 26˚C for 3h


title: RNA sequencing of pir1∆ pat1-as2 diploid cells_26C_1h

source_name: cells growing in EMM with 25µM 1-NM-PP1 at 26˚C for 1h


title: RNA sequencing of pir1∆ pat1-as2 diploidcells

source_name: cells growing in YEA at 26˚C


title: RNA sequencing of red1∆ pat1-as2 diploid cells_26C_4h

source_name: cells growing in EMM with 25µM 1-NM-PP1 at 26˚C for 4h


title: RNA sequencing of WT pir1-WT cells 2

source_name: cells growing in YEA at 30˚C


title: RNA sequencing of WT pat1-as2 diploid cells

value: WT pat1-as2 diploid cells


title: RNA sequencing of red1∆ pat1-as2 diploid cells_26C_4h_EMM-N


title: RNA sequencing of red1∆ pat1-as2 diploidcells


title: RNA sequencing of WT pat1-as2 diploid cells_26C_8h


title: RNA sequencing of pir1∆ pat1-as2 diploid cells_26C_4h


title: RNA sequencing of WT pat1-as2 diploid cells_26C_4h


title: RNA sequencing of WT pat1-as2 diploid cells_26C_6h


title: RNA sequencing of red1∆ pat1-as2 diploid cells_26C_2h

source_name: cells growing in EMM with 25µM 1-NM-PP1 at 26˚C for 2h


title: RNA sequencing of WT pat1-as2 diploid cells_26C_3h


title: RNA sequencing of red1∆ pat1-as2 diploid cells_26C_3h


title: RNA sequencing of pir1∆ pat1-as2 diploid cells_26C_2h


title: RNA sequencing of red1∆ pat1-as2 diploid cells_26C_5h


title: COVID9

source_name: Frontal cortex of brain

value: Frontal cortex of brain

tag: Sex

value: F


title: RNA sequencing of WT pat1-as2 diploid cells_26C_2h


title: RNA sequencing of WT pat1-as2 diploid cells_26C_7h


title: RNA sequencing of WT pat1-as2 diploid cells_26C_5h


title: RNA sequencing of WT pat1-as2 diploid cells_26C_1h


title: RNA sequencing of red1∆ pat1-as2 diploid cells_26C_1h


title: RNA sequencing of WT pat1-as2 diploid cells_26C_4h_EMM-N


title: RNA sequencing of WT pat1-as2 diploid cells_26C


title: RNA sequencing of WT cells_2

value: wild type h90 cells


title: RNA sequencing of tor2-ts6 ddb1∆ pir1∆ cells

value: tor2-ts6 ddb1_delta pir1_delta h90 cells


title: RNA sequencing of tor2-ts6 ubi4∆ cells

value: tor2-ts6 ubi4_delta h90 cells


title: RNA sequencing of pir1∆ cells

value: pir1_delta mat1Msmt0 cells


title: RNA sequencing of tor2-ts6 cul4∆ pir1∆ cells

value: tor2-ts6 cul4_delta pir1_delta h90 cells


title: RNA sequencing of WT cells_1

value: wild type mat1Msmt0 cells


title: RNA sequencing of tor2-ts6 cells_1

value: tor2-ts6 mat1Msmt0 cells


title: Thymocytes, 16036X4 KO1

status: Public on Dec 30 2019

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: Emma Eccles Jones, Medical Research Building, 15 North Medical Drive East

department: Pathology, Microbiology & Immunology

institute: University of Utah

data_processing:
Demultiplex with cellranger version 3.0.2 to create fastq files: I1 sample index, R1 cell barcode and UMI, R2 RNA sequence
Align reads to refdata-cellranger-mm10-3.0.0 from 10x Genomics and count barcodes and UMIs using cellranger count with expected-cells=5000
Genome_build: mm10
Supplementary_files_format_and_content: Filtered feature-barcode matrices in TSV and MTX format from cellranger count.

source_name: DAPI negative FACS sorted thymocytes

extract_protocol:
DAPI negative thymocytes were FACS sorted from homogenized and RBC lysed thymi of 6-10 week old Female MPC1fl/fl (WT) and Vav-Cre MPC1fl/fl (KO).
10X Genomics Single Cell 5' Gene Expression Reagent Kit

value: Vav-Cre MPC1 fl/fl

value: Thymus

value: DAPI negative FACS sorted thymocytes


title: RNA sequencing of tor2-ts6 ubi4∆ pir1∆ cells

value: tor2-ts6 ubi4_delta pir1_delta h90 cells


title: RNA sequencing of tor2-ts6 cul4∆ cells

value: tor2-ts6 cul4_delta h90 cells


title: RNA sequencing of tor2-ts6 cells_2

value: tor2-ts6 h90 cells


title: Thymocytes, 16036X5 KO2


title: RNA sequencing of tor2-ts6 ddb1∆ cells

value: tor2-ts6 ddb1_delta h90 cells


title: Thymocytes, 16036X1 W1

value: MPC1 fl/fl


title: Thymocytes, 16036X2 W2


title: Thymocytes, 16036X3 W3


title: Thymocytes, 16036X6 KO3


title: RNA sequencing of red1∆ pat1-as2 diploid cells_26C_6h

value: red1_delta pat1-as2 diploid cells


title: Direct-zol Kit isolated 20min heat Rep4

status: Public on Aug 07 2019

city: Fayetteville

middle: A.

last: Lewis

state: AR

address: 850 W. Dickson St.

department: Biological Sciences

institute: University of Arkansas

data_processing:
Reads were trimmed of adapter and low quality reads using Trimmomatic with the following paramaters: ILLUMINACLIP:< adapter fasta file (KAPA SI Sets A and B + Illumina TruSeq)>:2:30:10 LEADING:3 TRAILING:3 MAXINFO:40:0.4 MINLEN:40.
Trimmed reads were mapped to the S288c genome (Ensembl sacCer3; Saccharomyces_cerevisiae.R64-1-1.84.gtf) using STAR allowing for up to 49-bp overhangs.
Transcripts per million (TPM) and expected counts were obtained from RSEM with the parameter --strandedness reverse.
Differential expression was performed in EdgeR using expected counts and the quasi-liklihood (QL) framework with Benjamini-Hochberg FDR correction. To control for differences in sequencing depth across samples, the edgeR function thincounts was used to randomly subsample counts across all samples to be equal to the sample with the lowest number of total counts (8,678,188). Genes with less than 1 count per million (CPM) were excluded from the analysis.
Genome_build: sacCer3
Supplementary_files_format_and_content: abundance (TPM)
Supplementary_files_format_and_content: logFC and FDR-corrected p-values

organism: Saccharomyces cerevisiae

source_name: cell culture

growth_protocol: Cells were grown at 30°C in synthetic complete (SC) medium for >8 generations to an OD600 of 0.3.  Three technical replicate samples unstressed cells were collected, and then 55°C degree prewarmed media was added to directly increase the temperature to 37°C. Three technical replicate samples were collected following 20 minutes of heat shock.

extract_protocol:
Each technical replicate had RNA extracted by one of three methods: 1) hot phenol from Gasch, Methods in Enzymology, 2002, followed by cleanup with a Qiagen RNeasy column including optional on-column DNase digestion, 2) Qiagen RNeasy kit including optional on-column DNase digestion; 3) Zymo research Direct-zol kit
RNA-seq libraries were prepared from polyA-enriched RNA using the KAPA Biosystems mRNA HyperPrep Kit (KK8581) and KAPA Single-Indexed Adapter Set A+B (KK8700). All libraries were constructed in a single batch through an automated Eppendorf epMotion 5075 liquid handling robot

treatment_protocol: 55°C degree prewarmed media was added to directly increase the temperature to 37°C. Cells were incubated at 37°C for 20 minutes.

tag: protocol

value: Direct-zol Kit isolated 20min heat


title: Direct-zol Kit isolated 20min heat Rep3

growth_protocol: Cells were grown at 30°C in YPD synthetic complete (SC) medium for >8 generations to an OD600 of 0.3.  Three technical replicate samples unstressed cells were collected, and then 55°C degree prewarmed media was added to directly increase the temperature to 37°C. Three technical replicate samples were collected following 20 minutes of heat shock.


title: Direct-zol Kit isolated unstressed Rep4

value: Direct-zol Kit isolated unstressed


title: Direct-zol Kit isolated 20min heat Rep2


title: RNeasy Kit isolated 20min heat Rep3

value: RNeasy Kit isolated 20min heat


title: RNeasy Kit isolated 20min heat Rep4


title: Direct-zol Kit isolated unstressed Rep1


title: Direct-zol Kit isolated unstressed Rep2


title: Direct-zol Kit isolated unstressed Rep3


title: Direct-zol Kit isolated 20min heat Rep1


title: RNeasy Kit isolated 20min heat Rep2


title: Tumor Infiltrating Lymphocytes, 15885F2_1 NRE1-KO

status: Public on Oct 01 2019

data_processing:
I1 read: contains the sample index.
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
Demultiplex with cellranger mkfastq version 3.0.0 from 10x Genomics to create fastq files: I1 sample index, R1 cell barcode and UMI, R2 RNA sequence
Align reads to refdata-cellranger-mm10-3.0.0 from 10x Genomics and count barcodes and UMIs using cellranger count version 3.0.0 with expected-cells=5000
Genome_build: mm10
Supplementary_files_format_and_content: Filtered feature-barcode matrices in TSV and MEX format from cellranger count.

growth_protocol: Mice WT or lacking the Nampt NRE1 were injected with a B16F10 melanoma cell line to elicit immune cell infiltration of resulting tumors.

extract_protocol: Tumors were mechanically disrupted using frosted end of microscope slides and treated with Accumax (Innovative Cell Technologies, CA) for 45 minutes as done previously (Ekiz et al., 2019). Homogenized tumors were pooled per genotype and samples were stained with fluorophore conjugated anti-CD45 antibodies for 15 minutes in PBS containing 0.5% BSA and 2 mM EDTA followed by flow cytometric sorting. DAPI-negative live CD45+ cells were sorted and used for single cell RNA sequencing via 10X platform (High-throughput Genomics Core, University of Utah).

treatment_protocol: Excision of tumors in WT or NRE-KO mice at endpoint and isolation of CD45 positive immune cells from tumors.

tag: ID

tag: treatment

value: injected with B16F10 melanoma cell line to elicit immune cell infiltration of resulting tumors

value: B16F10 melanoma tumor infiltrating immune cells


title: Tumor Infiltrating Lymphocytes, 15885F1_1 WT

extract_protocol: Tumors were mechanically disrupted using frosted end of microscope slides and treated with Accumax (Innovative Cell Technologies, CA) for 45 minutes as done previously (Ekiz et al., 2019). Homogenized tumors were pooled per genotype and samples were stained with fluorophore conjugated anti-CD45 antibodies for 15 minutes in PBS containing 0.5% BSA and 2 mM EDTA followed by flow cytometric sorting. DAPI-negative live CD45+ cells were sorted and used for single cell RNA sequencing via 10X platform (High-throughput Genomics Core, University of Utah).TO BE UPDATED.

value: WT


title: RNeasy Kit isolated 20min heat Rep1


title: RNeasy Kit isolated unstressed Rep4

value: RNeasy Kit isolated unstressed


title: RNeasy Kit isolated unstressed Rep3


title: RNeasy Kit isolated unstressed Rep1


title: Phenol isolated 20min heat Rep2

value: Phenol isolated 20min heat


title: RNeasy Kit isolated unstressed Rep2


title: Phenol isolated 20min heat Rep3


title: Phenol isolated 20min heat Rep4

growth_protocol: Cells were grown at 30°C in synthetic complete (SC) medium) for >8 generations to an OD600 of 0.3.  Three technical replicate samples unstressed cells were collected, and then 55°C degree prewarmed media was added to directly increase the temperature to 37°C. Three technical replicate samples were collected following 20 minutes of heat shock.


title: Phenol isolated 20min heat Rep1


title: Phenol isolated unstressed Rep4

value: Phenol isolated unstressed


title: Phenol isolated unstressed Rep1


title: Phenol isolated unstressed Rep3


title: Phenol isolated unstressed Rep2


title: B134T61

status: Public on Jun 18 2019

city: Paris

first: Olivier

last: KOSMIDER

address: 27 Rue du faubourg Saint Jacques

country: France

institute: Institut Cochin

library_source: genomic

data_processing:
Reads were mapped to the human reference genome Hg19, using TopHat (v2.0.6).
Read count normalizations, differential gene expression analysis and differential junction read counts were performed using DESeq2.
Assuming that a maximum of 80% of genes are expressed, we selected the 20% lowest counts for each sample as background. A threshold was fixed at two standard deviations over the mean of the background. All transcripts for which normalized counts were lower than the computed threshold were designated as background for each array. When comparing normalized counts between two groups, a transcript was included in the analysis if its counts exceeded the background in at least 80% of the sample from at least 1 group.
To identify differentially expressed transcripts, we used empirical Bayes estimation. For the differential expression study, the results obtained after DESeq2 comparison were selected for further analysis and filtered at P ≤ 0.05 and fold-changes of 1.2, 1.5, or 2.
Read counts for splicing junctions from junctions.bed TopHat output were considered. Differential analysis of junctions was performed using DESeq2 (13). Only alternative acceptor splice sites (two or more 30ss with junctions to the same 50ss) and alternative donor splice sites (two or more 50ss with junctions to the same 30ss) were considered for this analysis. Predictions and analysis of branch point sequences were done with the online tools SVM-BPfinder (http://regulatorygenomics.upf.edu/ Software/SVM_BP/) and the Human Splicing Finder (http://www.umd.be/HSF/). The SVM_BP code was altered to allow for BP six base pairs from the 3′ss by setting minidist3ss=6 in svm_getfeat.py.
Genome_build: Human reference genome Hg19 RefSeq (RNA sequences, GRCh37), UCSC
Supplementary_files_format_and_content: Fastq and mapped.bam files.

source_name: Bone marrow mononuclear cells

extract_protocol:
Bone marrow mononuclear cells were purified on Ficoll gradient and processed for nucleic acid extraction using the DNA/RNA Kit (Qiagen). cDNA synthesis was conducted with MuLV Reverse Transcriptase (Invitrogen), with quality controls conducted on an Agilent 2100 Bioanalyzer (Agilent).
Libraries were constructed using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) and sequenced on an Illumina HiSeq 2500 platform using a 100-bp paired-end sequencing strategy.

tag: sample type

value: Screening sample

value: Bone marrow mononuclear cells

tag: genotype/variation

value: SF3B1 mutated


title: B134T57


title: B134T54

value: SF3B1 wildtype


title: B134T53


title: B134T51


title: B134T59


title: B133-B136T47


title: B133-B136T45


title: B133-B136T41


title: B133-B136T38


title: B133-B136T36


title: B134T49


title: B133-B136T43


title: B133-B136T33


title: B132T23


title: B132T26


title: B132T20


title: B132T29


title: B131T7


title: B131T9


title: B131T14


title: B132T17


title: B131T1


title: B131T4


title: B131T16


title: B131T13


title: B130T66


title: 14838X18

status: Public on Apr 30 2019

data_processing:
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 90.
The reference database was created using STAR version 2.5.2b with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Reads mapping uniquely to features in the Ensembl mouse GTF were counted using featureCounts version 1.5.1.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.18
Genome_build: GRCm38 (mouse)
Supplementary_files_format_and_content: Raw counts (featureCounts output files combined into a single tab-delimited matrix).

growth_protocol: WT Bone Marrow cells differentiated in vitro with M-CSF

extract_protocol:
Total RNA was isolated with miRneasy mini kit, library was prepped.
Library preparation used Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold.

treatment_protocol: Bone Marrow Macrophages treated in triplicate for 12 hr exposure to 50 ng/mL IFNg, 10 µM FK-866 and/or 10µM NMN

value: Bone Marrow Macrophage

value: IFNg, FK-866, NMN


title: 14838X15

value: media, FK-866, NMN


title: 14838X16


title: 14838X14


title: 14838X17


title: 14838X13


title: 14838X12

value: IFNg, FK-866


title: 14838X11


title: 14838X9

value: media, FK-866


title: 14838X8


title: 14838X7


title: 14838X6

value: IFNg


title: 14838X10


title: 14838X5


title: 14838X4


title: 14838X2

value: media


title: 14838X3


title: 14838X1


title: Gastric mucosae without Helicobacter pylori infection O4

status: Public on Dec 23 2019

city: Chuo-ku

first: Satoshi

last: Yamashita

state: Tokyo

address: Tsukiji 5-1-1

country: Japan

institute: National Cancer Center Research Institute

description: biopsy, gastric mucosae

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: Genome Studio software (V2011.1 Methylation module 1.9.0) was used.  Beta values were obtained after background correction and normalization to internal controls.

label: Cy5 and Cy3

source_name: Gastric mucosae 12

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA samples were isolated using Phenol-chloroform extraction protocol.

tag: gender

value: Male

tag: giemsa staining

tag: urea breath test

value: ND

tag: rapid urease test

tag: anti-hp igg antibody test

value: - (serum)

tag: pepsinogen


title: AMYG-4

status: Public on Oct 18 2018

city: Indianapolis

first: Jeanette

middle: Nance

last: McClintick

state: IN

address: 635 Barnhill Dr.

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

hyb_protocol: samples were hybridized to the Human Gene 1.0 ST GeneChips® for 17 hours then washed, stained and scanned with the standard protocol

scan_protocol: Chips scanned with the standard protocol using Affymetrix GeneChip® GCOS to generate data (CEL files)

data_processing: Affymetrix GeneChip® GCOS to generate data (CEL files).CEL files were imported into Partek Genomics Suite 7 (Partek, Inc., St. Louis, Mo) for analysis. RMA  (Robust multichip average, Bolstad, 2003) expression levels were generated for all probe sets using the RMA background correction, Quantile normalization and summarization by Median Polish. Summarized signals for each probe set were log2 transformed.

label: Biotin

source_name: amygdala

label_protocol: Samples were labeled using the Affymetrix Whole-Transcript labeling protocol starting with 100 ng of total RNA.

extract_protocol: RNA was extracted using Trizol (Invitrogen), with a higher ratio of Trizol to tissue to improve yield and purity (Edenberg et al., 2005), and further purified using RNeasy mini-columns (Qiagen, Valencia, CA).

tag: tissue

value: brain

tag: brain region

value: amygdala

tag: phenotype

value: control

value: male

tag: case


title: CERE-4

source_name: cerebellum

value: cerebellum


title: C-4

source_name: caudate nucleus

value: caudate nucleus


title: Gastric mucosae with Helicobacter pylori infection Y2

description: biopsy, gastric mucosae

source_name: Gastric mucosae 06

tag: age

value: + (serum)


title: THAL-4

source_name: thalamus

value: thalamus

tag: Sex


title: VCX-4

source_name: visual cortex

value: visual cortex


title: Gastric mucosae with Helicobacter pylori infection O2

description: biopsy, gastric mucosae

source_name: Gastric mucosae 14

value: Female


title: CCX-4

source_name: cerebral cortex

value: cerebral cortex


title: P-3

source_name: putamen

value: putamen

value: female


title: Gastric mucosae with Helicobacter pylori infection O4

description: biopsy, gastric mucosae

source_name: Gastric mucosae 16


title: Gastric mucosae without Helicobacter pylori infection O1

description: biopsy, gastric mucosae

source_name: Gastric mucosae 09


title: HIPPO-4

source_name: hippocampus

value: hippocampus


title: Gastric mucosae with Helicobacter pylori infection Y3

description: biopsy, gastric mucosae

source_name: Gastric mucosae 07


title: PFC-4

source_name: prefrontal cortex

value: prefrontal cortex


title: AMYG-3


title: CERE-3


title: C-3


title: HIPPO-3


title: Gastric mucosae without Helicobacter pylori infection O3

description: biopsy, gastric mucosae

source_name: Gastric mucosae 11

value: Male

value: ND

value: - (urine)


title: Gastric mucosae without Helicobacter pylori infection Y1

description: biopsy, gastric mucosae

source_name: Gastric mucosae 01


title: Gastric mucosae with Helicobacter pylori infection O1

description: biopsy, gastric mucosae

source_name: Gastric mucosae 13


title: Gastric mucosae without Helicobacter pylori infection Y2

description: biopsy, gastric mucosae

source_name: Gastric mucosae 02


title: Gastric mucosae without Helicobacter pylori infection Y3

description: biopsy, gastric mucosae

source_name: Gastric mucosae 03


title: Gastric mucosae without Helicobacter pylori infection Y4

description: biopsy, gastric mucosae

source_name: Gastric mucosae 04


title: Gastric mucosae with Helicobacter pylori infection O3

description: biopsy, gastric mucosae

source_name: Gastric mucosae 15


title: VCX-3

value: brain


title: Gastric mucosae with Helicobacter pylori infection Y1

description: biopsy, gastric mucosae

source_name: Gastric mucosae 05


title: P-4

value: control


title: THAL-2

source_name: thalamus

value: alcoholic


title: C-2

source_name: caudate nucleus


title: Gastric mucosae without Helicobacter pylori infection O2

description: biopsy, gastric mucosae

source_name: Gastric mucosae 10

value: - (serum)


title: THAL-3


title: PFC-3


title: P-2

source_name: putamen


title: HIPPO-2


title: Gastric mucosae with Helicobacter pylori infection Y4

description: biopsy, gastric mucosae

source_name: Gastric mucosae 08


title: CCX-2

source_name: cerebral cortex


title: CCX-3


title: VCX-2

source_name: visual cortex


title: P-1

value: male


title: AMYG-2

source_name: amygdala

value: amygdala


title: CERE-1

source_name: cerebellum

value: cerebellum


title: CCX-1


title: HIPPO-1

source_name: hippocampus


title: VCX-1

value: visual cortex


title: CERE-2


title: PFC-2

source_name: prefrontal cortex


title: THAL-1

value: thalamus


title: wobble2

status: Public on Nov 27 2017

city: Melbourne

first: Franco

last: Caramia

state: Victoria

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Alignment was performed using Bowtie2 Align (version 2.2.3) and TopHat (version 2.0.13)
Quantification performed using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: quantified RNA counts in TXT file

source_name: Prostate cancer cell line

growth_protocol: DU145 cells transduced with shE6AP or wobble controls were cultured in DMEM supplemented with 10% fetal calf serum and 1% penicillin/ streptomycin

extract_protocol:
RNA was extracted using TRIzol, as per manufacturers' instructions
Library was prepared using the TruSeq RNA library preparation kit version 2 using standard Illumina protocols

treatment_protocol: Knockdown of E6AP was induced in the presence of 0.2 μg/ml doxycycline for 2.5 days

tag: cell line

tag: transduced with short hairpin against

value: control against E6AP


title: wobble1


title: PFC-1


title: wobble3


title: AMYG-1


title: C-1

value: caudate nucleus


title: shE6AP3


title: shE6AP1


title: shE6AP2


title: Mock Replicate 2 (nascent rna-seq)

status: Public on Jun 28 2017

first: Dale

last: Dorsett

address: 1100 South Grand Boulevard

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

description:
nascent RNA
mock.plus.norm.sgr
mock.minus.norm.sgr

data_processing:
Basecalling was performed by Torrent Suite version 4 and 5 software using the default settings
The fastq files were aligned in two steps. First, they were aligned to a fasta file containing the Drosophila melanogaster release 5.9 pre-rRNA, ncRNA, and miscRNA sequences using TMAP map4 algorithm with 5' and 3' softclipping and a minimum seed length of 20. The reads that did not align were selected using samtols and aligned to the Drosophila melanogaster genome sequence without allowing clipping. The aligned reads were sorted and indexed using samtools and genome coverage was calculated using BEDTools.
The total gene sequence coverage was calculated and used to normalize coverage across all samples. Normalized bedgraph files were generated using BEDTools and converted to sgr files as described in Pherson et al, submitted.
Genome_build: Drosophila melanogaster release 5 (April 2006) with chrU and U_extra sequences removed
Supplementary_files_format_and_content: Normalized plus strand and minus strand sgr files of nascent RNA reads
[Expression.Table.txt, columns L-R, V-W] File with normalized sequencing coverage of all annotated genes and statistical comparison of expression in RNAi treated cells to Mock RNAi control cells.

organism: Drosophila melanogaster

source_name: ML-DmBG3-c2 cultured cells

growth_protocol: BG3 cells were cultured in Schneider's media with 10% FCS and 10 μg per ml insulin.

extract_protocol:
Chromatin was prepared for nascent RNA isolation as described in Weber et al. 2014 Mol Cell 53: 819-30. doi:10.1016/j.molcel.2014.02.014. The chromatin pellet was dissolved in 10 mL Trizol (Invitrogen) and RNA was isolated following the manufacturer's protocol and precipitated by isopropanol with 0.2M NaCl and 20 micrograms of glycogen. Nascent RNA was digested with DNaseI (Epicentre) and uncapped RNAs were degraded in a two step reaction to remove ribosomal RNA, and residual mRNAs were depleted using oligo d(T) dynabeads (Ambion) as decribed in Pherson et al, submitted.
Ion Xpress IonXpressRNA barcoded sequencing libraries were constructed using Ion Total v2 kits (Life Technologies) according to the manufacturer's directions, with modifications to allow for separate 5' and 3' adapter ligation steps. First, the 3' adapter was ligated to capture native 3' ends of the nascent RNA, followed by RNase III treatment, and 5' adapter ligation as described in Pherson et al, submitted. The remaining steps of reverse transcription and PCR amplification were followed as described by the manufacturer.

treatment_protocol: For RNAi, media was replaced with 1 ml of Express Five SFM (Invitrogen) with 1% FCS, (and 10 μg per ml insulin for BG3 cells), for 3 hours. For RNAi of all factors, from 0.7 to 40 μg of dsRNA was added per well of a 6-well plate. Media was adjusted to 3 ml and 10% FCS withSchneider's media after 2 hrs of RNAi treatment. Cells were replated as needed. Templates for dsRNA synthesis were made by PCR from cDNA or genomic DNA templates using primers with T7 promoters. In most experiments, equal amounts of two dsRNAs against each target were used. Both individual dsRNAs knocked down the targets, but knockdown was generally more efficient with a mixture. Templates were designed to avoid off-target matches of ≥19 nucleotides using Drosophila RNAi Screening Center (http://www.flyrnai.org/) online tools.

tag: RNAi treatment

value: Mock RNAi treatment


title: Mock Replicate 3 (nascent rna-seq)


title: Ph RNAi Replicate 1 (nascent rna-seq)

description:
nascent RNA
iPh.plus.norm.sgr
iPh.minus.norm.sgr

value: Ph RNAi treatment


title: Ph RNAi Replicate 3 (rna-seq)

data_processing:
Basecalling was performed by Torrent Suite version 4 and 5 software using the default settings
Alignment to Drosophila melanogaster genome sequence was performed using TMAP map4 algorithm with 5' and 3' softclipping and a minimum seed length of 20 nt
The total sequencing base pair coverage in all exons was summed for all annotated genes in each sample and normalized to total coverage using bedtools and custom R as described in Wu et al. 2015 PLoS Genetics Nov 6;11(11):e1005655.
Genome_build: Drosophila melanogaster release 5 (April 2006) with chrU and U_extra sequences removed
Supplementary_files_format_and_content: [Expression.Table.txt, columns B-K, S-U] File with normalized sequencing coverage of all annotated genes and statistical comparison of expression in RNAi treated cells to Mock RNAi control cells.

extract_protocol:
Total RNA was extracted using the Zymo Research Quick-RNA MicroPrep Kits with DNaseI treatment following the manufacturer's directions.
Ion Xpress IonXpressRNA barcoded sequencing libraries were constructed using the Eukaryotic Ribominus and Ion Total v2 kits (Life Technologies) according to the manufacturer's directions.


title: Ph RNAi Replicate 2 (nascent rna-seq)


title: Ph RNAi Replicate 2 (rna-seq)


title: Mock Replicate 3 (rna-seq)


title: Mock Replicate 2 (rna-seq)


title: Ph RNAi Replicate 1 (rna-seq)


title: Mock Replicate 1 (nascent rna-seq)


title: Mock Replicate 4 (rna-seq)


title: Mock Replicate 5 (rna-seq)


title: Mock Replicate 1 (rna-seq)


title: Mock Replicate 6 (rna-seq)


title: ybaO over-expression, rep2

status: Public on Jun 13 2017

city: Richardson

first: Zhenyu

last: Xuan

state: TX

address: 800 West Campbell

institute: UT Dallas

description: E coli strain W3110 with cutR plasmid

hyb_protocol: Affymetrix Technical Manual, Prokaryotic Sample and Array Processing

data_processing: The CEL files are processed by RMA in Bioconductor package Affy.

organism: Escherichia coli

source_name: ybaO over-expression

growth_protocol: Cells were grown in Luria-Bertani (LB) medium until reaching OD600 of 0.3

extract_protocol: Total RNA

treatment_protocol: Cells were challenged with 1 mM cysteine for 30 minutes, and then harvested

tag: strain

tag: genotype

value: ybaO over-expression


title: ybaO over-expression, rep3

description: E coli strain W3110 with cutR plasmid

scan_protocol: Affymetrix Technical Manual, Prokaryotic Sample and Array Processing


title: ybaO over-expression, rep1

description: E coli strain W3110 with cutR plasmid

label_protocol: Affymetrix Technical Manual, Prokaryotic Sample and Array Processing


title: ybaO deletion, rep1

description: E coli strain W3110 with cutR genomic deletion

source_name: ybaO deletion

value: ybaO deletion


title: ybaO deletion, rep2


title: KT, biological rep 3

status: Public on Apr 10 2017

city: Ciudad de México

first: Ricardo

last: Orozco-Solis

state: TLALPAN

address: Periférico Sur 4809, Arenal Tepepan

country: Mexico

institute: Instituto Nacional de Medicina Genomica

description:
ketamine (3 mg/kg) at ZT 5
0515F-01_12

hyb_protocol: 100 ng of total RNA per sample was used as a template to obtain cDNA with the GeneChip cDNA synthesis Kit (Affymetrix, Santa Clara, CA). Mouse Gene ST arrays 2.0 (Affymetrix) were used to determine the transcriptome expression levels in the three groups of mice.

scan_protocol: The arrays were scanned in the GeneChip Scanner 3000 7G (Affymetrix) and the Command Console Software was used to produce the .CEL intensity file.

data_processing:
Data were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP). (Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).
affymetrix-algorithm-name = plier-gene-full
affymetrix-algorithm-version = 2.0
program-name = Expression Console
program-version = 1.1.2800.28061

label: TdT

source_name: ketamine (3 mg/kg), (ZT 5)

label_protocol: The fragmented single-stranded DNA is labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin

extract_protocol: Immediately after euthanization, brains were extracted, frozen in dry ice and stored at -80°C. The anterior cingulate cortex was microdissected (Bregma 1.34 to -0.5 mm). Total RNA was extracted from each sample using TRIzol (Invitrogen, Carlsbad, CA) following manufacturer´s instructions scaled 1:10. Total RNA was resuspended in 30 ul of RNase free water and quantified using a NanoDrop spectrophotometer (Wilmington, DE). About 5 ul was used for QPCR experiments. The remaining TRIzol-extracted RNA was diluted to 100 ul final volume of RNase-free water and cleaned using the Quiagen RNeasy Mini purification kit (Redwood, CA), following the manufacturer’s protocol. Eluted RNA was quantified with a nano-drop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE). The quality of the RNA was assessed on an Agilent Bioanalyzer 2100 (Santa Clara, CA).

treatment_protocol: KT-treated mice were injected with a KT solution of 3 mg/kg, i.p. at ZT 5.Control mice was injected i.p. with saline solution in a volume of 100ul/0.03 kg at ZT 5. Mice housed in the circular cage were kept awake for 12 hours (ZT 0 to ZT 12) by a slowly rotating bar (1.5 rpm), suspended 1 cm above the floor and bedding within the mouse cage

tag: strin

tag: treated with

value: ketamine (3 mg/kg)

tag: treatment time

value: ZT 5

tag: harvest time point

value: ZT 13

value: Anterior Cingulate Cortex


title: SD, biological rep 3

description:
sleep derivation 12 hrs (ZT0-ZT12)
0515F-01_8

source_name: sleep deprivation (ZT0-ZT 12)

value: sleep deprivation

value: ZT 0 to ZT 12


title: Ph RNAi Replicate 3 (nascent rna-seq)


title: KT, biological rep 2

description:
ketamine (3 mg/kg) at ZT 5
0515F-01_11


title: SD, biological rep 1

description:
sleep derivation 12 hrs (ZT0-ZT12)
0515F-01_6


title: SD, biological rep 2

description:
sleep derivation 12 hrs (ZT0-ZT12)
0515F-01_7


title: KT, biological rep1

description:
ketamine (3 mg/kg) at ZT 5
0515F-01_10


title: Saline, biological rep 3

description:
saline solution at ZT 5
0515F-01_4

source_name: saline solution (ZT 5)

value: saline solution


title: Brg1_ChIP-seq

status: Public on Sep 14 2016

data_processing:
Fastq reads were mapped to mouse genome mm9 with bowtie 0.12.7
Duplicated reads from mapping were removed by picard-tools 1.127
Brg1 binding peaks were detected by SICER version 1.1
The peak regions were liftovered to mm10 in order to compare with ChIP-seq data of other transcription factors
Genome_build: mm10
Supplementary_files_format_and_content: bed format of peak regions

source_name: SmoM2 medulloblastoma_primary tumor

growth_protocol: Spontaneous medulloblastoma formed in CAG-CreER, Rosa26-SmoM2 mice.

extract_protocol:
Dissociated medullblastoma cells are crosslinked, lysed and sonicated. The nuclear lysates were immunoprecipitated with anti Brg1/Brm antibodies.
NEBNext ChIP-Seq Sample Prep Master Mix Set 1 was used for library generation and a Hiseq 2500 sequencer was used for sequencing at UT Southwestern Medical Center Sequencing Core Facility

value: medulloblastoma

tag: mouse genotype

value: CAG-CreER, Rosa26-SmoM2

tag: antibody

value: Brg1/Brm (J1) (Khavari et al., 1993).


title: RNAseq_Brg1KO

data_processing:
Fastq reads were mapped by Tophat1.4.1 to mouse genome mm10
Cuffdiff 2.1.1 was used to identify differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: Cufflink gene expression output fpkm for each gene

source_name: SmoM2 medulloblastoma primary tumor Brg1 knockout

growth_protocol: Spontaneous medulloblastoma formed in CAG-CreER, Rosa26-SmoM2, Brg1+/+ or CAG-CreER, Rosa26-SmoM2, Brg1F/F mice.

extract_protocol:
Total RNA was extracted using TRIzol from  dissected medulloblastoma tissues
RNA-seq libraries were prepared using the Illumina RNA-Seq Preparation Kit and were sequenced on a HiSeq 2000 sequencer at UT Southwestern Sequencing Core Facility.

treatment_protocol: Tamoxifen injection for 10 times every other day.

tag: tissue

value: CAG-CreER, Rosa26-SmoM2, Brg1F/F

tag: treatment

value: tamoxifen injection


title: Brg1_input

value: none (input)


title: RNAseq_WT

source_name: SmoM2 medulloblastoma primary tumor

value: CAG-CreER, Rosa26-SmoM2, Brg1+/+


title: Saline, biological rep 2

description:
saline solution at ZT 5
0515F-01_2


title: Saline, biological rep 1

description:
saline solution at ZT 5
0515F-01_1


title: ybaO deletion, rep3


title: female_control_136

status: Public on Sep 05 2013

hyb_protocol: Standard Affymetrix protocol for Gene ST type arrays

scan_protocol: Scanned using Affymetrix GCOS

data_processing: Partek 6.3 was used to generate the RMA data, using the core probesets only option. This option generated the 'core' probesets as defined by Affymetrix as well-defined. This option generated 28,869 probe sets. Using the CEL files you may generate the rest, but these 28,869 probe sets were all that was used for the analysis.  RMA signals were generated for the core probe sets using the RMA background correction, Quantile normalization and summarization by Median Polish. Summarized signals for each probe set were log2 transformed. These are the standard defaults used in Partek.

label_protocol: WT protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay, rev. 5

extract_protocol: Trizol using 2 times recommended volume, followed by Qiagen RNeasy column

tag: phenotype

value: control

tag: gender

value: female

value: postmortem hippocampus

tag: cirrhosis

value: N

tag: smoker

tag: post-mortem-interval (hrs)

tag: brain ph at time of freezing


title: male_control_139

value: male

tag: age

value: Yes


title: female_control_133

value: No


title: female_alcoholic_135

value: alcoholic

value: Y


title: male_control_140


title: male_alcoholic_137


title: male_alcoholic_134


title: female_control_138


title: female_alcoholic_132


title: male_control_130

value: Ex


title: male_alcoholic_128


title: male_control_129


title: female_control_131


title: male_control_127


title: male_alcoholic_124


title: male_alcoholic_121


title: male_control_123


title: male_control_125


title: female_alcoholic_126


title: female_alcoholic_122


title: female_alcoholic_114


title: male_control_113


title: female_alcoholic_118


title: female_control_116


title: male_alcoholic_119


title: Wilms10_P7

status: Public on Jun 01 2016

city: Duesseldorf

first: Brigitte

last: Royer-Pokora

address: Universitätsstr. 1

institute: Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x GE hybridization buffer HI- RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (4x 44K) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) and air dried.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Scans were quantified using Agilent Feature Extraction Software (batch A: V10.7.1.1; batch B: V11.5.1.1) applying default parameters. Control spots were removed, replicate oligos averaged. Arrays were quantile normalized between chips using R-software (Limma).

source_name: Wilms10 tumor cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were cultivated in MCSG-medium (Lonza) at 37 degree and 5% CO2.  Medium was changed every third day.

extract_protocol: RNA was prepared using the RNAeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations, with an included on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Batch B: The cell culture of Wilsm10 was immortalized with telomerase (pBABE-hygro hTERT- from Addgene) and a triple mutant SV40 large T antigen (U19 del89-97tsA58). Both construct were transduced into Wilms10 cells using a  retroviral virus. After transduction the cells were cultured in G418 (selection for T-antigene; 200µg/ml)  for a week, followed with hygromycin (selection for telomerase; 20 µg/ml). In addition single cell clones were isolated and cultivated initially at 33 degree for maintenance of the temperature sensitive T-Antigene.

value: kidney

tag: batch

value: A

tag: cell line

value: tumor cell line of patient Wilms10


title: male_alcoholic_115


title: Wilms10_P3


title: male_alcoholic_117


title: male_alcoholic_120


title: male_alcoholic_107


title: th:GFP_96h_GFPminus control

status: Public on Oct 15 2012

city: Freiburg

first: Wolfgang

last: Driever

address: Hauptstrasse 1

department: Biology

institute: University of Freiburg

description:
Sample_11_MM_th:GFP_96h_GFPminus
Sample processed for polyA mRNA Seq
MM_thGFP_96h_RNASeq.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Samples 1 through 4: sequence data are in read files from two lanes using bar codes (vmatGFPminus - ATCGTG; vmatGFPplus - AGTATA; otpGFPminus - AGTAGC; otpGFPplus - AGTACG); Samples 5 though 12 sequence data are in separate read files each
Fastq sequencing data  were imported with NGS-Illumina import. For this import the quality score was set to “Illumina pipline 1.5 to 1.7”
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using CLC Genomics Workbench v4.8
Sequences were mapped to genome with CLC Genomics Workbench v4.8 built48014 using menue "high thriughput sequencing" and mapping settings minimal fraction length 0.9, minimum similarity fraction 0.8, maximum number of hitts for read 10
Expression values were calculated as RPKM using CLC Genomics Workbench v4.8
Statistical analysis were performed using the Test on proportions => Kal et al.‘s test (Z-test) using CLC Genomics Workbench v4.8
Genome_build: Zebrafish reference genome ZV9.66
Supplementary_files_format_and_content: Excel spreadsheets with output generated from CLC Genomics Workbench v4.8; each spreadsheet  provides data analysis for comparison of one GFP plus experimental and one GFP minus control sample

organism: Danio rerio

source_name: FACS sorted cells from whole embryo

growth_protocol: Zebrafish were gown under standard condition 28 Celsius

extract_protocol:
RNA was extracted from FACS sorted cells as descried in: Manoli and Driever, 2012, Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633
Samples 1 through 4 were processed for NanoCAGE (Salmullah et al., CSH Protocols 2011, DOI 10.1101/pdb.prot5559); Samples 5 through 12 were processed for mRNA Seq (Manoli and Driever, 2012, Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633) including an amplification step using Ambion RNA amp kit as described in CSH Protocol.

treatment_protocol: Cells were dissociated and FACS sorted as described in: Manoli and Driever, 2012, Cold Spring Harbor Protoc. DOI 10.1101/pdb.prot069633

tag: developmental stage

value: 96 hrs post fertilization

tag: transgenic line

value: th:GFP BAC

tag: facs sorting criteria

value: GFP negative cells


title: th:GFP_96h_GFPplus sorted catecholaminergic neurons

description:
Sample_12_MM_th:GFP_96h_GFPplus
Sample processed for polyA mRNA Seq
MM_thGFP_96h_RNASeq.xlsx

value: GFP positive cells


title: th:GFP_72h_GFPplus sorted catecholaminergic neurons

description:
Sample_10_MM_th:GFP_72h_GFPplus
Sample processed for polyA mRNA Seq
MM_thGFP_72h_RNASeq.xlsx

value: 72 hrs post fertilization


title: th:GFP_72h_GFPminus control

description:
Sample_9_MM_th:GFP_72h_GFPminus
Sample processed for polyA mRNA Seq
MM_thGFP_72h_RNASeq.xlsx


title: thGal4_UAS:GFP_36h_GFPminus control

description:
Sample_5_MM_thGal4_UAS:GFP_36h_GFPminus
Sample processed for polyA mRNA Seq
MM_thGal4_UASGFP_36h_RNASeq.xls

value: 36 hrs post fertilization

value: th:Gal4VP16 driver and UAS:EGFP responder


title: thGal4_UAS:GFP_48h_GFPplus sorted catecholaminergic neurons

description:
Sample_8_MM_thGal4_UAS:GFP_48h_GFPplus
Sample processed for polyA mRNA Seq
MM_thGal4_UASGFP_48h_RNASeq.xls

value: 48 hrs post fertilization


title: male_control_112

value: control

value: male

value: postmortem hippocampus

value: N


title: male_alcoholic_111

value: alcoholic

value: Y


title: thGal4_UAS:GFP_48h_GFPminus control

description:
Sample_7_MM_thGal4_UAS:GFP_48h_GFPminus
Sample processed for polyA mRNA Seq
MM_thGal4_UASGFP_48h_RNASeq.xls


title: thGal4_UAS:GFP_36h_GFPplus sorted catecholaminergic neurons

description:
Sample_6_MM_thGal4_UAS:GFP_36h_GFPplus
Sample processed for polyA mRNA Seq
MM_thGal4_UASGFP_36h_RNASeq.xls


title: male_control_109

value: Yes


title: otpb:GFP_24h_GFPplus sorted catecholaminergic neurons

description:
Sample_4_MM_otpb:GFP_24h_GFPplus
Samples processed for NanoCAGE
MM_otpb_GFP_24h_NanoCAGE.xls

data_processing:
Library strategy: RNA-Seq (NanoCAGE)
Illumina Casava1.7 software used for basecalling.
Samples 1 through 4: sequence data are in read files from two lanes using bar codes (vmatGFPminus - ATCGTG; vmatGFPplus - AGTATA; otpGFPminus - AGTAGC; otpGFPplus - AGTACG); Samples 5 though 12 sequence data are in separate read files each
Fastq sequencing data  were imported with NGS-Illumina import. For this import the quality score was set to “Illumina pipline 1.5 to 1.7”
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using CLC Genomics Workbench v4.8
Sequences were mapped to genome with CLC Genomics Workbench v4.8 built48014 using menue "high thriughput sequencing" and mapping settings minimal fraction length 0.9, minimum similarity fraction 0.8, maximum number of hitts for read 10
Expression values were calculated as RPKM using CLC Genomics Workbench v4.8
Statistical analysis were performed using the Test on proportions => Kal et al.‘s test (Z-test) using CLC Genomics Workbench v4.8
Genome_build: Zebrafish reference genome ZV9.66
Supplementary_files_format_and_content: Excel spreadsheets with output generated from CLC Genomics Workbench v4.8; each spreadsheet  provides data analysis for comparison of one GFP plus experimental and one GFP minus control sample

value: 24 hrs post fertilization


title: male_alcoholic_105


title: otpb:GFP_24h_GFPminus control

description:
Sample_3_MM_otpb:GFP_24h_GFPminus
Samples processed for NanoCAGE
MM_otpb_GFP_24h_NanoCAGE.xls


title: female_control_110

value: female


title: vmat2:GFP_24h_GFPminus control

description:
Sample_1_MM_vmat2:GFP_24h_GFPminus
Samples processed for NanoCAGE
MM_vmat2_GFP_24h_NanoCage.xlsx


title: vmat2:GFP_24h_GFPplus sorted catecholaminergic neurons

description:
Sample_2_MM_vmat2:GFP_24h_GFPplus
Samples processed for NanoCAGE
MM_vmat2_GFP_24h_NanoCage.xlsx


title: male_control_101

value: No


title: male_control_106


title: male_alcoholic_103


title: male_control_104


title: male_alcoholic_108


title: Wilms5_rep1

status: Public on Feb 01 2010

description: US45103065_251485018486_S02_GE1-v5_95_Feb07_1_1.txt

hyb_protocol: 1.65 ug of Cy3-labeled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x GE hybridization buffer HI- RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (4x 44K) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) and air dried.

scan_protocol: Slides were scanned with an Agilent Technologies Scanner G2505B using a scan area of 61x21.6 mm, scan resolution of 5µm, dye channel set to green and green PMT set to 100%.

data_processing: Scans were quantified using Agilent Feature Extraction V10.1.1.1 Software using default parameters (protocols GE1-V5_91 and GE1-V5_95, as indicated by raw data file names). Control spots are removed, replicate oligos are averaged.

source_name: Wilms tumor cell line 5 replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: For all Wilms (primary Wilms tumor cultures from different patients) and MSC samples: cells were cultivated in MSCB-medium supplemented with Bullet Kit (Lonza). For CLS1 samples: cells were cultivated in Iscoves medium supplemented with 2mM L-Glutamine and 15% FCS. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the RNAeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendation with an included on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: kidney

value: 1 year 11 month

tag: cell type

value: Wilms tumor cell line

tag: genome/variation

value: WT1 mut


title: Wilms5_rep3

description: US45103065_251485038458_S01_GE1-v5_95_Feb07_1_1.txt

source_name: Wilms tumor cell line 5 replicate 3


title: CLS1_rep4

description: US45103065_251485018482_S01_GE1-v5_95_Feb07_1_4.txt

source_name: Wilms tumor cell line CLS1 replicate 4

value: 5 years

value: Wilms tumor cell line CLS1


title: Wilms3_rep1

description: US22502668_251485010291_S01_GE1-v5_91_0806_1_2.txt

source_name: Wilms tumor cell line 3 replicate 1

value: 11 month


title: Wilms3_rep4

description: US45103065_251485038458_S01_GE1-v5_95_Feb07_1_2.txt

source_name: Wilms tumor cell line 3 replicate 4


title: CLS1_rep2

description: US45103065_251485018482_S01_GE1-v5_95_Feb07_1_2.txt

source_name: Wilms tumor cell line CLS1 replicate 2


title: Wilms2_rep4

description: US22502668_251485010289_S01_GE1-v5_91_0806_1_3.txt

source_name: Wilms tumor cell line 2 replicate 4

value: 12 month

value: WT1/CTNNB1 mut


title: Wilms4_rep1

description: US45103065_251485018486_S02_GE1-v5_95_Feb07_1_2.txt

source_name: Wilms tumor cell line 4 replicate 1

value: male


title: CLS1_rep3

description: US45103065_251485018482_S01_GE1-v5_95_Feb07_1_3.txt

source_name: Wilms tumor cell line CLS1 replicate 3


title: Wilms3_rep2

description: US22502668_251485010288_S01_GE1-v5_91_0806_1_1.txt

source_name: Wilms tumor cell line 3 replicate 2


title: Wilms4_rep2

description: US45103065_251485018486_S02_GE1-v5_95_Feb07_1_4.txt

source_name: Wilms tumor cell line 4 replicate 2


title: Wilms4_rep3

description: US45103065_251485038459_S01_GE1-v5_95_Feb07_1_4.txt

source_name: Wilms tumor cell line 4 replicate 3


title: CLS1_rep1

description: US45103065_251485018482_S01_GE1-v5_95_Feb07_1_1.txt

source_name: Wilms tumor cell line CLS1 replicate 1


title: Wilms3_rep3

description: US22502668_251485010289_S01_GE1-v5_91_0806_1_1.txt

source_name: Wilms tumor cell line 3 replicate 3


title: Wilms1_rep3

description: US22502668_251485010290_S01_GE1-v5_91_0806_1_4.txt

source_name: Wilms tumor cell line 1 replicate 3


title: Wilms2_rep2

description: US22502668_251485010288_S01_GE1-v5_91_0806_1_4.txt

source_name: Wilms tumor cell line 2 replicate 2


title: Wilms2_rep1

description: US22502668_251485010291_S01_GE1-v5_91_0806_1_3.txt

source_name: Wilms tumor cell line 2 replicate 1


title: Wilms1_rep2

description: US22502668_251485010288_S01_GE1-v5_91_0806_1_3.txt

source_name: Wilms tumor cell line 1 replicate 2


title: Wilms1_rep1

description: US22502668_251485010291_S01_GE1-v5_91_0806_1_4.txt

source_name: Wilms tumor cell line 1 replicate 1


title: Wilms2_rep5

description: US45103065_251485038458_S01_GE1-v5_95_Feb07_1_3.txt

source_name: Wilms tumor cell line 2 replicate 5


title: Wilms5_rep2

description: US45103065_251485018486_S02_GE1-v5_95_Feb07_1_3.txt

source_name: Wilms tumor cell line 5 replicate 2


title: Wilms1_rep4

description: US22502668_251485010289_S01_GE1-v5_91_0806_1_4.txt

source_name: Wilms tumor cell line 1 replicate 4