title: SAL125_1876267_Scap KO_Tumor Treg_rep2

description: sgRNA transduced OT-I cells


title: EPAS_MO_ 2

status: Public on Feb 24 2021

type: SRA

city: Lund

first: Sofie

last: Mohlin

address: TCR, MV404:C3, Scheelevagen 8

department: Clinical Sciences

country: Sweden

institute: Lund University

library_source: transcriptomic

data_processing:
Demultiplexing: organized the FASTQ files based on the sample index information, and generated the statistics and reporting files. This task was performed using the bcl2fastq2 software with default settings
Raw Quality Control (QC): FastQC provided quality control analyses and checked on raw sequence data coming from the above Demultiplexing step of the pipeline.
Read Mapping: alignment of reads to the specified reference genome. This task was performed using the HISAT2 software package, and the reference genome sequence was from the Ensemble database, the Gallus Gallus 5.0, and the annotation (GTF) from the release 92.
Mapping QC: mapping quality control checked such as evaluating the distribution of reads mapped by the above mapping step.
Expression counts: assembled the alignments into full transcripts and quantified  the expression levels of each gene and transcript. This task was performed using the StringTie software package.
DE analysis: Differentially expressed genes (DEG) analysis was performed using DESeq2.
Genome_build: Gallus Gallus 5.0,
Supplementary_files_format_and_content: tab-separated text files generated by StringTie software package; contains expression counts

molecule: total RNA

organism: Gallus gallus

source_name: Chick embryo derived trunk neural crest cells

growth_protocol: Embryos were allowed to grow in an incubator set at 37.5°C until stage HH16 was reached.

extract_protocol:
RNA was extracted using Ambion RNAqueous Micro Kit (AM1931)
Library was prepared according to TruSeq® Stranded mRNA Sample Preparation Guide (Part # 15031047 Rev. E) Modification of “Enrich DNA Fragment” step: from 15 to 13 PCR cycles.
TruSeq® Stranded mRNA Library Prep

treatment_protocol: Embryos were injected and electroporated with morpholinos at stage HH10+.

tag: cell type

value: Trunk neural crest cells

tag: modification

value: EPAS1 morpholino

tag: age (hh stage)


title: EPAS_MO_ 1


title: EPAS_MO_ 10


title: EPAS_MO_ 3


title: SAL122_1876264_WT_Tumor Treg_rep4

type: RNA

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

country: USA

institute: St Jude Children's Research Hospital

description: sgRNA transduced OT-I cells

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Clariom S mouse GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

organism: Mus musculus

source_name: Treg cells from the B16 melanoma-bearing mice

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Tregs were sorted from lymph node/tumor from the B16 melanoma tumor and MC38 colon adenocarcinoma, and Tregs were sorted from pheripheral lymph node from WT mice.

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

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

tag: background strain

value: Foxp3-YFP+ cells

tag: cell population

value: tumor infiltrating Treg

tag: tissue source

value: B16 melanoma tumor

tag: genotype

value: WT


title: SAL111_1876253_WT_LN Treg_rep4

description: sgRNA transduced OT-I cells

source_name: Treg from Lymph node of WT mice bearing no tumors.

value: lymph node Treg

value: lymph node


title: SAL110_1876252_WT_LN Treg_rep3

description: sgRNA transduced OT-I cells


title: SAL121_1876263_WT_Tumor Treg_rep3

description: sgRNA transduced OT-I cells


title: SAL127_1876269_Scap KO_Tumor Treg_rep3

description: sgRNA transduced OT-I cells

value: Scap KO


title: CTRL_MO_8

value: 5'-mispair morpholino (control)


title: 7d3-1-RNA

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

data_processing:
Sequencing reads were trimmed by trim galore v0.6.5 with default parameters. Trimmed ChIP-seq reads were mapped to the mm10 genome with bowtie2 v2.4.1. Peaks were called using MACS2 v2.2.7.1 (q < 0.05). Mapped reads from ChIP and input samples were extended by 100 bp on either side (250 bp total) and a normalized signal was calculated. For visualization in IGV v2.8.12 (Broad Institute), the signal was calculated in 100bp windows over the entire genome and output as a bigWig file.
Enhancer regions were predicted by identifying H3K27ac(high) regions that did not intersect with promoters (defined as TSS +/- 2000bp). Consensus H3K27ac peak sets were generated for each experimental group (VEH, 24 h, 48 h and 7d) using Diffbind v3.0.5 and then combined together to generate a temporary pool. Peak widths were expanded to be 1000 bp (summit +/-500bp) and H3K27ac peak regions that intersected with promoters were removed. ChIP-seq reads were counted within each enhancer region under Diffbind default conditions. Differential enhancers between any two experimental groups were extracted from the temporary pool using the bioconductor DESeq2 v1.30.0 package (FDR<0.05) with Benjamini-Hochberg method.
K-means clustering: K-means clustering was performed on differential enhancers and dynamically expressed genes across experimental groups. In each row, the values (x) were normalized by dividing by √(sum(x^2)). The optimal number of clusters was determined using the silhouette method.
Identification of genes targeted by enhancers: We created a list of the enhancer target genes by examining the correlation between gene expression (as reflected by RNA-seq data) and H3K27ac intensity at the candidate enhancers. Comparing to assigning an enhancer to its nearest gene, this approach produces a much higher percentage of enhancer-gene pairs that match the results determined experimentally using techniques including Hi-C. All the enhancers that were not linked with their target genes after the step were then processed using ChIPSeeker v1.26.0 with default condition and TxDb.Mmusculus.UCSC.mm10.knownGene to link to their nearest genes (as target genes). All the target genes identified, either by correlation between H3K27ac and RNA-seq or by linking with nearest genes, were combined for downstream analysis.
Gene ontology (GO) term and transcription factor (TF) motif analysis: GO biological processes enrichment test was performed using the bioconductor clusterProfiler package v3.18.0 (with FDR adjusted p-value < 0.01). Motif analysis was also performed to determine enriched transcription factor binding motifs among the enhancer regions using Homer v4.11 (with options –size 200 –p 16, and q-value < 0.01).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are converted by wigToBigWig. Raw couns of sequencing reads were generated by featureCounts.

source_name: Neuron from the frontal lobes of the mouse cortex

extract_protocol:
Nuclei extraction: All steps were conducted on ice, and all centrifugation was conducted at 4 °C. One piece of mouse frontal cortex tissue (6-10 mg) was placed in 3 ml of ice-cold nuclei extraction buffer (NEB) [0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM tris-HCl, and 0.1%(v/v) Trition X-100] with freshly added 30 µl of protease inhibitor cocktail (PIC, Sigma-Aldrich), 3 µl of 100 mM phenylmethylsulfonyl fluoride (PMSF, Sigma-Aldrich) in Isopropyl alcohol, 3 µl of 1 M dithiothreitol (DTT, Sigma-Aldrich), and 4.5 µl of ribonuclease (RNase) inhibitor (2313A,Takara Bio). The tissue was homogenized in tissue grinder (D9063, Sigma-Aldrich). The homogenate was filtered with a 40 µm cell strainer (22-363-547, Thermo Fisher Scientific) and collected in a 15-ml centrifuge tube. The cell suspension was centrifuged at 1000 RCF for 10 min. The supernatant was discarded, and the pellet was resuspended in 0.5 ml of ice-cold NEB with freshly added 5 µl of PIC, 0.5 µl of PMSF, 0.5 µl of DTT, and 0.75 µl of RNase inhibitor. 500 µl of the sample was mixed with 750 µl of 50%(w/v) iodixanol (made by mixing 4 ml of OptiPrepTM gradient (Sigma-Aldrich) and 0.8 ml of diluent [150 mM KCl, 30 mM MgCl2, and 120 mM tris-HCl]). The mixture was centrifuged at 10,000 RCF for 20 min. Then, the supernatant was removed and 300 µl of 2%(w/v) normal goat serum (50062Z, Life technologies) in Dulbecco’s PBS (DPBS, Life technologies) was added to resuspend the nuclei pellet. To separate NeuN+ and NeuN- fractions, 6 µl of 2 ng/µl anti-NeuN antibody conjugated with Alexa 488 (MAB377X, Millipore) in DPBS was added into the nuclei suspension. The suspension was mixed well and incubated at 4 °C for 1 h on a rotator mixer (Labnet). After incubation, the sample was sorted into NeuN+ and NeuN- fractions using a BD FACSAriaTM cell sorter (BD Biosciences). The sorted NeuN+ nuclei were directly used for RNA-seq experiment. 200 µl of sorted NeuN+ nuclei suspension, containing ~26,000 nuclei, was added into 800 µl of ice-cold PBS for ChIP-seq experiment. 200 µl of 1.8 M sucrose solution, 10 µl of 1 M CaCl2, and 3 µl of 1 M Mg(Ac)2 were added into the mixture. The solution was mixed well and incubated on ice for 15 min. Then, the sample was centrifuged at 1800 RCF at 4 °C for 15 min. The supernatant was discarded and the pellet was resuspended in 60 µl of PBS with freshly added 0.6 µl of PIC and 0.6 µl of PMSF and stored on ice until use for ChIP-seq.
ChIP-seq library construction: ~10,000 NeuN+ nuclei were used to produce each ChIP-seq library and two technical replicates were generated for each brain sample. One input per sample was generated using ~4,000 nuclei. ChIP was carried out using multiplexed MOWChIP-seq with MNase digestion for chromatin fragmentation and anti-H3K27ac (39135, Active Motif) antibody, following a published protocol (Zhu et al., Nature Protocols 14 (2019) 3366-3394.). RNA-seq library construction: ~5000 NeuN+ nuclei were used to produce each RNA-seq library and two technical replicates were generated for each brain sample. RNA extraction from 50 µl of nuclei suspension from FACS (containing 5000 sorted NeuN+ nuclei) was conducted using RNeasy Mini Kit (74104, Qiagen) and RNase-Free DNase Set (79254, Qiagen), following the manufacturer’s instruction. Extracted mRNA in 30-µl volume was concentrated by ethanol precipitation and resuspended in 4.6 µl of RNase-free water. cDNA was prepared using SMART-seq2 protocol (Picelli et al., Nature Protocols 9 (2014) 171–181.) with minor modification. ~2 ng of mRNA in 4.6 µl of water was mixed with 2 µl of 100 µM oligo-dT primer and 2 µl of 10 mM dNTP mix. After being denatured at 72 °C for 3 min, the mRNA solution was immediately placed on ice. 11.4 µl of reverse transcript mix [made from 1 µl of SuperScript II reverse transcriptase (200 U/µl), 0.5 µl of RNAse inhibitor (40 U/µl), 4 µl of Superscript II first-strand buffer, 1 µl of DTT (100mM), 4 µl of 5 M Betaine, 0.12 µl of 1 M MgCl2, 0.2 µl of TSO (100 µM), 0.58 µl of nuclease-free water] was mixed with the mRNA solution and the mixture was incubated at 42 °C for 90 min, followed by 10 cycles of (50 °C for 2 min, 42 °C for 2 min). The reaction was finally inactivated at 70 °C for 15 min. 20 µl of first-strand mixture was then mixed with 25 µl of KAPA HiFi HotStart ReadyMix, 0.5 µl of (100 µM) IS PCR primers, 0.5 µl of Evagreen dye, and 4 µl of nuclease-free water. Generated cDNA was amplified by incubated at 98 °C  for 1 min, followed by 9-11 cycles of (98 °C 15 s, 67 °C 30 s, 72 °C 6 min). After PCR amplification, 50 µl of PCR mix was purified by using 50 µl of SPRIselect beads. ~600 pg of purified cDNA was used to produce a RNA-seq library using Nextera XT DNA Library Preparation kit (FC-131-1024, Illumina), following the manufacturer instructions.

tag: age

value: 12 weeks

tag: strain

tag: treatment

value: amphetamine (2,5-dimethoxy-4-iodoamphetamine [DOI] injection)

tag: time point

value: 7 days


title: 7d3-2-RNA


title: 7d4-2-RNA


title: 7d4-1-RNA


title: SAL109_1876251_WT_LN Treg_rep2

description: sgRNA transduced OT-I cells


title: CTRL_MO_3


title: CTRL_MO_7


title: CTRL_MO_1


title: CTRL_MO_4


title: 7d2-2-RNA


title: 7d1-1-RNA


title: 7d1-2-RNA


title: 48h4-2-RNA

value: 48 hours


title: 7d2-1-RNA


title: 48h3-2-RNA


title: C4 cell line - exosomes

city: 重庆

first: Yutong

last: Wu

address: 高滩岩正街30号

country: China

institute: Third Military Medical University

data_processing:
The fastx_toolkit (0.0.14) software was used to dynamically remove the linker sequence fragments and low-quality fragments from the 3'end of the sequencing data.
Use seqtk (1.0-r82-dirty) and self-written R (3.x.x) scripts to perform quality control analysis on the preprocessed data.
Small RNA classification uses unitas software, and sequence alignment uses bowtie (1.0.0).
Genome_build: hg19
Supplementary_files_format_and_content: .xlsx files include microRNA expression.

organism: Homo sapiens

source_name: C4 cells line

growth_protocol: The cell line was cultured in serum-free medium to collect the supernatant, and the extracellular vesicles (EVs) were collected by differential centrifugation following MISEV2018 guidelines.

extract_protocol:
Use miRNeasy Serum/Plasma Kit(50) Qiagen#217184 kit for RNA extraction of samples, and follow the standard operating procedure manual provided by the kit manufacturer during extraction.The extraced total RNA is the sample.
Libraries were prepared for sequencing using standard QiagenTM miRNA library construction protocol.

tag: cell line

value: human prostate cancer cell line

tag: molecule subtype

value: exosomal RNA


title: 48h2-2-RNA


title: 48h3-1-RNA


title: 48h2-1-RNA


title: Wild-type-20gy-Day6-Rep2 [WT-IR-2]

city: New York City

first: Marco

last: Tigano

address: 540 First Avenue

institute: NYU Grossman School of Medicine

description:
C3_3-WT-IR
processed data file:
MCF10_DEcompare_WTvsRHO_Irradiated.txt
MCF10_IRmtDNA_normalizedCounts.txt
MCF10_IRmtDNA_rawCounts.txt

data_processing:
Read quality check, FASTQC
Alignment to reference genome, STAR
Transcript quantification, HTSeq
Normalization and DE Analysis, DeSeq2
Genome_build: hg19
Supplementary_files_format_and_content: Normalized transcript counts in txt, Raw transcript counts in txt, DE comparison output from DeSeq2 in txt

molecule: polyA RNA

extract_protocol:
RNAeasy Mini Kit, Qiagen
NEBNext® Ultra™ II RNA Library Prep Kit for Illumina

treatment_protocol: 20 gy IR delivered at 0.8gy/min with CellRad350 Faxitron.

tag: cell line/type

value: wild-type

value: Irradiated

tag: source molecule

value: total cellular RNA


title: rho0-20gy-Day6-Rep2 [rho0-IR-2]

description:
D3_3-ddC-IR
processed data file:
MCF10_DEcompare_WTvsRHO_Irradiated.txt
MCF10_IRmtDNA_normalizedCounts.txt
MCF10_IRmtDNA_rawCounts.txt

value: rho zero


title: SAL108_1876250_WT_LN Treg_rep1

description: sgRNA transduced OT-I cells

value: Foxp3-YFP+ cells


title: 48h1-1-RNA


title: 48h1-2-RNA


title: Wild-type-20gy-Day6-Rep1 [WT-IR-1]

description:
C2_2-WT-IR
processed data file:
MCF10_DEcompare_WTvsRHO_Irradiated.txt
MCF10_IRmtDNA_normalizedCounts.txt
MCF10_IRmtDNA_rawCounts.txt


title: 48h4-1-RNA


title: PC3 cell line - exosomes

source_name: PC3 cells line


title: Dloop Active - Rep 2 [DL-2]

description:
processed data file:
DLOOPvsNT.xlsx
DLOOPvsDEAD.xlsx
ARPE19_mtDSB_normalizedCounts.txt
ARPE19_mtDSB_rawCounts.txt

data_processing:
Read quality check, FASTQC
Alignment to reference genome, STAR
Transcript quantification, HTSeq
Normalization and DE Analysis, DeSeq2
Genome_build: hg19
Supplementary_files_format_and_content: Differentially Expressed genes from DeSeq2, Excel Format. Raw reads count, normalized counts.

source_name: Dloop Active

extract_protocol:
RNAeasy Mini Kit, Qiagen
NEBNext Ultra RNA Library Prep kit, New England Biolabs

treatment_protocol: Transfection of plasmid DNA with Lipofectamine 3000 (Thermo Fischer Scientific)

value: Transfected - mtDNA DSB


title: 24h3-2-RNA

value: 24 hours


title: 24h4-2-RNA


title: 24h4-1-RNA


title: C4-2B cell line - exosomes

source_name: C4-2B cell line


title: Dloop Active - Rep 2 [DL-3]


title: rho0-20gy-Day6-Rep1 [rho0-IR-1]

description:
D2_2-ddC-IR
processed data file:
MCF10_DEcompare_WTvsRHO_Irradiated.txt
MCF10_IRmtDNA_normalizedCounts.txt
MCF10_IRmtDNA_rawCounts.txt


title: Dloop Active - Rep 1 [DL-1]


title: ATP8 Dead - Rep 2 [X-2]

description:
processed data file:
DEADvsNT.xlsx
ATP8vsDEAD.xlsx
DLOOPvsDEAD.xlsx
ARPE19_mtDSB_normalizedCounts.txt
ARPE19_mtDSB_rawCounts.txt

source_name: ATP8 Dead

value: Transfected - WT mtDNA


title: 24h3-1-RNA


title: ATP8 Dead - Rep 3 [X-3]


title: 24h2-2-RNA


title: 24h2-1-RNA


title: ATP8 Active - Rep 3 [CD5-3]

description:
processed data file:
ATP8vsNT.xlsx
ATP8vsDEAD.xlsx
ARPE19_mtDSB_normalizedCounts.txt
ARPE19_mtDSB_rawCounts.txt

source_name: ATP8 Active


title: ATP8 Active - Rep 2 [CD5-2]


title: 24h1-2-RNA


title: 24h1-1-RNA


title: Non Transfected - Rep 1 [NT-1]

description:
processed data file:
ATP8vsNT.xlsx
DEADvsNT.xlsx
DLOOPvsNT.xlsx
ARPE19_mtDSB_normalizedCounts.txt
ARPE19_mtDSB_rawCounts.txt

source_name: Non Transfected

value: Non Transfected


title: VEH4-2-RNA

value: vehicle


title: VEH3-2-RNA


title: VEH4-1-RNA


title: VEH3-1-RNA


title: VEH2-1-RNA


title: VEH2-2-RNA


title: 24h-input

library_source: genomic

molecule: genomic DNA

tag: antibody


title: 7d-input


title: VEH1-2-RNA


title: 7d6-1-K27ac

value: anti-H3K27ac (39135, Active Motif)


title: 7d6-2-K27ac

value: 12 weeks


title: VEH1-1-RNA


title: ATP8 Dead - Rep 1 [X-1]


title: 7d5-1-K27ac

value: amphetamine (2,5-dimethoxy-4-iodoamphetamine [DOI] injection)


title: 7d4-1-K27ac

value: 7 days


title: 7d3-2-K27ac


title: 7d3-1-K27ac


title: ATP8 Active - Rep 1 [CD5-1]


title: 7d2-1-K27ac


title: 7d2-2-K27ac


title: 7d1-1-K27ac


title: 7d1-2-K27ac


title: Non Transfected - Rep 2 [NT-2]


title: 48h6-1-K27ac

value: 48 hours


title: 48h4-2-K27ac


title: 48h4-1-K27ac


title: 48h-input


title: 48h5-1-K27ac


title: 48h3-2-K27ac


title: 7d4-2-K27ac


title: 24h6-1-K27ac


title: 24h6-2-K27ac


title: 48h1-1-K27ac


title: 48h5-2-K27ac


title: VEH-input


title: 48h2-2-K27ac


title: 24h5-1-K27ac


title: 24h5-2-K27ac


title: 7d5-2-K27ac


title: MCF7_hyp_r2

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

description:
MCF7 24h 1% hypoxia bruseq experiment 2
Bru-labeled RNA

data_processing:
Library strategy: Bru-seq
Illumina Casava v1.8.2 software used for basecalling.
Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using Bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1
Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.genes.bed: The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score (placeholder); (6) strand; (7) gene span; (8) feature_type (gene_sense represents the actual gene); (9) length (sum of feature lengths, e.g. introns and exons); (10) length (sum of feature lengths, e.g. introns and exons); (11) read count (sense or antisense strand); (12) density (RPK) – count/length; (13) RPKM - count/(length/1E3)/(mapped read count/1E6).

growth_protocol: MCF-7 cells were tested mycoplasma-free and maintained at 37°C in 5% CO2 with DMEM/High glucose medium supplemented with 10% (v/v) FBS and antibiotics.

extract_protocol:
Cells were labeled with 2 mM Bromouridine (Sigma Aldrich) for 30 min, total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013 (Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response. Proc. Natl. Acad. Sci. U.S.A. 2013; 110:2240–2245).
cDNA libraries were made from the BrU-labeled RNA using the Illumina TruSeq library kit and sequenced using Illumina HiSeq sequencers at the University of Michigan DNA Sequencing Core with 52 bp single-end reads (on average 50 million reads per sample including 70% unique reads). Sequencing and read mapping (unique reads only) were carried out as described using the human genome reference assembly hg19/GRCh37 (Paulsen et al., 2014).

treatment_protocol: One set of replicates were cultivated in hypoxia (1% O2) for 24 hours and the other set was grown in normoxia (21% O2) for the same period of time, before Bromouridine incubation and RNA isolation.

tag: condition

value: Hypoxia

tag: assay

value: BruSeq

tag: labeling agent

value: Bromouridine (Bru)

tag: bru labeling time

value: 0.5 hours

tag: time between end of bru labeling and rna extraction

value: 0 hours


title: MCF7_hyp_r1

description:
MCF7 24h 1% hypoxia bruseq experiment 1
Bru-labeled RNA


title: 48h3-1-K27ac


title: 48h6-2-K27ac


title: MCF7_ctl_r2

description:
MCF7 control bruseq experiment 2
Bru-labeled RNA

value: Normoxia


title: 24h2-1-K27ac


title: 24h3-1-K27ac


title: 24h4-2-K27ac


title: 24h4-1-K27ac


title: 24h2-2-K27ac


title: 24h3-2-K27ac


title: MCF7_ctl_r1

description:
MCF7 control bruseq experiment 1
Bru-labeled RNA


title: 48h1-2-K27ac


title: 48h2-1-K27ac


title: 130926  MV4;11_AS99_5µM_H3K36me2 Cut & Run

first: Fengbiao

last: Mao

address: 1301 Catherine St

department: Department of Pathology

data_processing:
Library strategy: CUT&RUN
Cut&Run sequencing reads were mapped to the hg19 genome for human by using Bowtie2 (v2-2.2.4) with parameters “-q --phred33  --very-sensitive -p 10”.
Then, we removed duplicated reads using SAMtools (v1.5). BAM files of mapping results were merged for the same sample using SAMtools and converted to BED format by using BEDTools.
Peaks regions were called for each sample by using MACS (v 1.4) from cutRun mapped reads with parameters "macs -t mapped.bed  -n sample_id -w -S -g hs -p 0.00001".
Homer v4.10 was employed to perform gene annotation of peaks and MACS2 was used to identify differential peaks.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: _peaks.xls: Excel files include peaks.

source_name: MV4;11 leukemia cell line

growth_protocol: MV4;11 human leukemia cells were cultured in RPMI-1640 supplemented with 10% heat inactivated FBS and 1% Penicillin/ Streptomycin.

extract_protocol:
Cut & Run experiments were performed using 2X10e6 cells treated with 5µM AS-99 or 0.25% DMSO for Ash1L or H3K36me2 antibodies, according to Cut & Run protocols.
Libraries were prepared with the Illumina TruSeq protocol according to the manufacturer’s protocol.

treatment_protocol: MV4;11 cells were treated with 5 µM AS-99 or 0.25% DMSO for 4 days.

tag: cell type

value: MV4;11 leukemia cell line


title: 130925  MV4;11_DMSO_H3K36me2 Cut & Run

value: DMSO


title: 130920  MV4;11_AS99_5µM_Ash1L Cut & Run


title: 130919  MV4;11_DMSO_Ash1L Cut & Run


title: VEH6-1-K27ac


title: VEH5-2-K27ac


title: VEH5-1-K27ac


title: VEH4-2-K27ac


title: VEH4-1-K27ac


title: 24h1-2-K27ac

value: 24 hours


title: VEH3-2-K27ac


title: VEH3-1-K27ac


title: VEH2-1-K27ac


title: 24h1-1-K27ac


title: C26-CHO 8

city: Brussels

first: Laure

last: Bindels

address: Avenue E. Mounier, 73 bte B1.73.11

department: Metabolism and Nutrition Research Group

country: Belgium

institute: Louvain Drug Research Institut

data_processing:
De-multiplexed using Illumina's bcl2fastq 2.17 software
Quality-controlled and trimming using FastQC tool and Trimmomatic Version 0.38
Read alignment using STAR Version 2.6.1d
Count matrices were generated from reads aligned to the reference genome (BAM files) using the function summarizeOverlaps from the R package GenomicAlignments and then tested for differential expression and normalized using the R package DESeq2 Version 1.22.2
Genome_build: Mus musculus GRCm38.75
Supplementary_files_format_and_content: Text file include normalized counts based on median-of-ratios method using DESeq2 for each sample.

source_name: C26 cachectic group treated with cholestyramine

extract_protocol:
Livers were removed, frozenin liquid nitrogen, and RNA was harvested using Trizol reagent. RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA). Excess DNA was removed by DNase I treatment (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: liver

tag: tumor

value: Yes

value: C26-injected mice receiving cholestyramine in their diet


title: C26-CHO 7


title: VEH6-2-K27ac

tag: age

value: anti-H3K27ac (39135, Active Motif)

value: vehicle


title: VEH2-2-K27ac

value: 12 weeks

tag: strain


title: VEH1-2-K27ac

tag: treatment


title: VEH1-1-K27ac


title: C26-CHO 6


title: C26-CHO 5


title: C26-CHO 4


title: C26-CHO 3


title: Control diet_skin_Pool3

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

description: Gene expression for fish fed with control diet (pool 3)

hyb_protocol: The hybridization protocol was carried out according to Agilent's instructions. Briefly, 1.65 μg of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/mg cRNA) was fragmented at 60°C for 30 min in a total reaction volume of 55 µl containing 25X Agilent fragmentation buffer and 10X Agilent blocking agent. On completion of the fragmentation reaction, 55 µl of 2X GEx hybridization buffer was added to the fragmentation mixture and hybridized to S. aurata array (ID 024502, Agilent) at 65°C and 10 rpm for 17 hours in a rotating hybridization oven.

scan_protocol: After hybridization, microarrays were washed 1 min at room temperature (RT) with GEWash Buffer 1 (Agilent), 1 min with GE Wash buffer 2 (Agilent) pre-incubated at 37°C, 45 s at RT with Acetonitrile (Sigma, St Louis, MO, USA), and 30 s at RT with stabilization and drying solution (Agilent). Slides were scanned immediately afterwashing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area: 61 x21.6 mm; Scan resolution: 5 µm; Dye channel set to green; Green PMT: 100%). Spot intensities and other quality control features were extracted with Feature Extraction software version 10.4.0.0 (Agilent).

data_processing: For microarray analysis, a percentile shift normalization was carried out and then data were filtered by expression (standard deviation) among groups. Then, gene-level analysis was conducted in order to obtain the median of signal intensities from spots within a probe set. Statistical test (t-test unpaired) was done with GeneSpring software GX 14.3 to obtain the differentially expressed genes (p-value < 0.05) between control and treatments.

organism: Sparus aurata

source_name: Control diet_skin

label_protocol: One-color microarray was carried out according to manufacturer’s protocols. Briefly, 200 ng of total RNA was reversed transcribed along with spike-in (Agilent One-Color RNA Spike-In kit, Agilent Technologies, USA). Then, the solution was used as template for Cyanine-3 (Cy3) labeled cRNA synthesis and amplification with the Low Input Quick Amp Labelling kit (Agilent).  Samples of cRNA were purified using the RNeasy micro kit (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted individually from fish skin using QIAGEN RNeasy® Mini Kit following the manufacturer's recommendations. The total RNA concentration was quantified using a NanoDrop ND-2000 (Thermo Scientific) and RNA integrity and quality checked with the Experion (Automated Electrophoresis Station, Bio-Rad) using the Experion Standard Sens RNA chip (Bio-Rad). Only the samples with an RNA integrity number (RIN) > 8.0 were chosen for further analysis.

treatment_protocol:
Gilthead seabream fry (average body size 9.5 g) were obtained from a commercial hatchery (Piscimar SL, Andromeda Group, Spain) and transported by road to IRTA-Sant Carles de la Rapita research facilities (Sant Carles de la Ràpita, Spain).
Fish were acclimated in two 2000-L tanks for two weeks. After their acclimation, all fish were anesthetized (tricaine methanesulfonate [MS-222], 150 mg/L) and individually weighed for initial body weight (BWi) and measured for standard length (SLi) to the nearest 0.1 g and 1 mm, respectively, and then distributed into eight 500-L cyclindroconical tanks at a density of 50 fish per tank (4 tanks/replicates per diet).   Fish (BWi = 10.6 ± 0.1 g, n = 400, mean ± standard deviation, SD) were fed for 95 days with both experimental diets by means of automatic feeders (ARVO-TEC T Drum 2000; Arvotec, Huutokosk, Finland) at the rate of 2.5% of the stocked biomass, which approached apparent satiation. Feed ration was evenly distributed in 7 meals per day from 08:00 to 18:00 h. Fish were regularly sampled at a monthly basis in order to evaluate their growth in BW and adjust the feeding ratio to stocked biomass. During the trial, water temperature and pH (pH meter 507; Crison Instruments, Barcelona, Spain), salinity (MASTER-20T; ATAGO Co., Ltd., Tokyo, Japan), and dissolved oxygen (OXI330; Crison Instruments) were 22.1 ± 0.4 °C, 7.0 ± 0.01, 36 mg/L, and 7.2 ± 0.3 mg/L (mean ± SD), respectively. Water flow rate in experimental tanks was maintained at approximately 9.0-10.1 L/min via a recirculation system (IRTAmar®; Spain) that maintained adequate water quality (total ammonia and nitrite were ≤0.15 and 0.6 mg/L, respectively) through UV, biological, and mechanical filtration. Photoperiod followed natural changes according to the season of the year (November to February; 40°37′41″ N).   At the end of the trial, fish were sacrificed with an overdose of MS-222 (200 mg/L) for tissue sampling purposes. Skin samples (1 cm2 of anterior dorsal body region) were dissected and immediately transferred into RNAlater (Ambion®), fixed overnight and then frozen at -80 °C until further RNA extraction.

value: Skin

value: juveniles, 82.7 ± 3.2 g

value: Control diet


title: SDPP diet_skin_Pool1

description: Gene expression for fish fed with SDPP diet (pool 1)

source_name: SDPP diet_skin

value: juveniles, 88.2 ± 1.6 g

value: SDPP diet


title: Control diet_skin_Pool1

description: Gene expression for fish fed with control diet (pool 1)


title: SDPP diet_skin_Pool2

description: Gene expression for fish fed with SDPP diet (pool 2)


title: Dorsal root ganglion cells-Control_rep5

city: Shanghai

first: Kaikai

last: Wang

address: 393 Middle Huaxia Road

institute: ShanghaiTech University

description:
raw_UMI_counts_4.txt
raw_UMI_counts_4_metadata.txt

data_processing:
Basecalls were performed using bcl2fastq2-v2.19.1.403
Sequenced reads of 10x genomics were processed using Cell Ranger (version.2.1.0) with default parameters
Sequenced reads of Smart-seq2 were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit (version 0.0.13), then mapped to mm10 using hisat2 (version: 2.0.4), finally,  the reads counts were normalized to FPKM (Fragments Per Kilobase of exon per Megabase of library size)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each single cell
Supplementary_files_format_and_content: tab-delimited text files include raw UNI counts for each single cell
Supplementary_files_format_and_content: tab-delimited text files include cell information

source_name: Dorsal root ganglion cells

extract_protocol:
For Smart-seq2, Total RNA was extracted with AMBION AM1560 kit; for 10x Genomics, The cellular suspensions were further processed with Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v2, 16 rxns PN-120237
RNA libraries were prepared for sequencing using standard Illumina protocols

value: untreated

value: Dorsal root ganglion

tag: technology

value: 10x genomics


title: 8h WT Treg in vitro rep2

source_name: Treg cells from the pheripheral Lymph node FoxCre-YFP (WT) mice

growth_protocol: Tregs were sorted from pheripheral lymph node from WT mice.

value: YFP+ cells from sort-purified CD4 T cells


title: Dorsal root ganglion cells-SNI 28d

value: SNI 28d


title: C26-CHO 1


title: SDPP diet_skin_Pool3

description: Gene expression for fish fed with SDPP diet (pool 3)


title: 0h WT Treg in vitro rep3


title: 8h WT Treg in vitro rep5


title: 8h WT Treg in vitro rep4


title: C26 7

source_name: C26 cachectic group

value: untreated C26-transplanted mice


title: Single Dorsal root ganglion neuron_Control [S758]

description:
S758
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

data_processing:
Basecalls were performed using bcl2fastq2-v2.19.1.403
Sequenced reads of 10x genomics were processed using Cell Ranger (version.2.1.0) with default parameters
Sequenced reads of Smart-seq2 were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit (version 0.0.13), then mapped to mm10 using hisat2 (version: 2.0.4), finally,  the reads counts were normalized to FPKM (Fragments Per Kilobase of exon per Megabase of library size)
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values, raw UNI counts for each single cell and cell information

value: Control

tag: tissue/cell type

value: Single Dorsal root ganglion neuron


title: Single Dorsal root ganglion neuron_Control [S757]

description:
S757
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: C26 6

value: liver

value: Yes


title: C26 8


title: 8h WT Treg in vitro rep3


title: 8h WT Treg in vitro rep1


title: Single Dorsal root ganglion neuron_Control [S756]

description:
S756
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Control diet_skin_Pool2

description: Gene expression for fish fed with control diet (pool 2)


title: 0h WT Treg in vitro rep2


title: 0h WT Treg in vitro rep5


title: Single Dorsal root ganglion neuron_Control [S755]

description:
S755
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 0h WT Treg in vitro rep1


title: C26-CHO 2

value: C26-injected mice receiving cholestyramine in their diet


title: Single Dorsal root ganglion neuron_Control [S753]

description:
S753
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: C26 3


title: Single Dorsal root ganglion neuron_Control [S751]

description:
S751
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_Control [S752]

description:
S752
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S749]

description:
S749
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

value: SNI 14d


title: C26 1


title: Single Dorsal root ganglion neuron_SNI 14d [S748]

description:
S748
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: CT 7

source_name: Control group

value: No

value: sham-injected mice


title: CT 6


title: Single Dorsal root ganglion neuron_SNI 14d [S747]

description:
S747
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: C26 2


title: 0h WT Treg in vitro rep4


title: C26 4


title: Single Dorsal root ganglion neuron_SNI 14d [S745]

description:
S745
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: CT 5


title: CT 4


title: Single Dorsal root ganglion neuron_SNI 14d [S746]

description:
S746
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: CT 3


title: CT 1


title: SAM24364586

city: South San Francisco

first: Mitchell

last: Rezzonico

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
For each sample, the R1 file provides the barcode representing the cell (positions 1-16) and the UMI (positions 17-24). The R2 file provides the insert sequence.
Single-cell RNA sequencing data were processed with an in-house analysis pipeline as described (CITE https://www.sciencedirect.com/science/article/pii/S2211124719317656). Reads were demultiplexed based on perfect matches to expected cell barcodes. Transcript reads were aligned to the mouse reference genome (GRCm38) using GSNAP (2013-10-10) (Wu and Nacu, 2010). Only uniquely mapping reads were considered for downstream analysis. Transcript counts for a given gene were based on the number of unique UMIs (up to one mismatch) for reads overlapping exons in sense orientation. Cell barcodes from empty droplets were filtered by requiring a minimum number of detected transcripts. Sample quality was further assessed based on the distribution of per-cell statistics, such as total number of reads, percentage of reads mapping uniquely to the reference genome, percentage of mapped reads overlapping exons, number of detected transcripts (UMIs), number of detected genes, and percentage of mitochondrial transcripts.
For each sample the R1 file provides the barcode representing the cell and the R2 file provides the insert sequence
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary file TsneCoordinatesAndClusterAssignments.txt contains sample ID and genotype for each cell, as well as tSNE coordinates, Seurat clustering and biological interpretations of Seurat clusters for all cells (columns allCells.*) and for microglial cells only (columns microglia.*) as described in manuscript.

extract_protocol:
Single cell suspensions were processed using Chromium™Single Cell 3’ Reagent Kits v2 (10X Genomics PN-120237 and PN-120236) following manufacturer’s user guide. Cell-RT mix was prepared to aim 10,000 cells per sample and applied to Chromium™ Controller for GEM generation and barcoding. Then samples were subjected to post GEM-RT cleanup, cDNA amplification (10 cycles), and library construction according to the user guide. Sample index PCR was done with 12 cycles. Libraries were then quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Q33230) and profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies 5067-4626). Libraries were sequenced by HiSeq4000 (Illumina) following 10X Genomics sequencing specification
cDNAs and libraries were prepared according to manufacturer instructions (10× Genomics)

tag: genotype group

value: Hippocampus


title: SAM24364585


title: Single Dorsal root ganglion neuron_SNI 14d [S742]

description:
S742
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_Control [S738]

description:
S738
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_Control [S736]

description:
S736
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_Control [S739]

description:
S739
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S743]

description:
S743
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: SAM24362778


title: CT 8


title: SAM24362777

source_name: NonTg


title: Single Dorsal root ganglion neuron_Control [S734]

description:
S734
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: SAM24362776


title: Single Dorsal root ganglion neuron_Control [S732]

description:
S732
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: SAM24362775


title: Single Dorsal root ganglion neuron_Control [S731]

description:
S731
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: SAM24362774


title: SAM24362772


title: Single Dorsal root ganglion neuron_SNI 14d [S744]

description:
S744
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: SAM24362773


title: Single Dorsal root ganglion neuron_Control [S723]

description:
S723
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_Control [S722]

description:
S722
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: SAM24362771


title: Single Dorsal root ganglion neuron_Control [S724]

description:
S724
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_Control [S726]

description:
S726
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_Control [S721]

description:
S721
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: SAM24362767


title: C26 5


title: Single Dorsal root ganglion neuron_SNI 14d [S717]

description:
S717
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S715]

description:
S715
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S716]

description:
S716
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S713]

description:
S713
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S712]

description:
S712
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S704]

description:
S704
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S700]

description:
S700
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S699]

description:
S699
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: p27wt.1

city: London

first: Karine

last: Rizzoti

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing:
The RSEM package (version 1.3.30) (Li and Dewey, 2011) was used in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl mouse GRCm.38.89 version transcriptome
Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package (version 1.18.1)  within the R programming environment (version 3.4.3)
Genome_build: Ensembl mouse GRCm.38.89
Supplementary_files_format_and_content: VST log2 normalised expression values. Rows = genes; Columns = samples.

source_name: intermediate lobe

extract_protocol:
Total mRNA was extracted from dissected pituitary intermediate lobes using the RNeasy Micro kit
cDNA was generated using Ovation RNA-seq System V2 (Tecan, 7102-A01), libraries were constructed using Ovation Ultralow System V2 (Tecan, 0344NB-A01) according to the manufacturer’s instructions. Libraries were quantified using the TapeStation (Agilent) and pooled in equimolar proportions. Library were sequenced on an Hiseq4000 (Illumina)

value: pituitary intermediate lobe

value: 2 to 3-month old

tag: genotype

value: WT


title: p27wt.2


title: p27wt.4


title: p27wt.3


title: SAM24362768


title: p27null.3


title: p27null.2


title: Single Dorsal root ganglion neuron_SNI 14d [S709]

description:
S709
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: S2CK

data_processing:
10X’s Cell Ranger software was used to de-multiplex Illumina BCL output, create fastq files and generate single cell feature counts
Raw reads were initially processed by the Cell Ranger v.3.0.2 pipeline, which deconvolved reads to their cell of origin using the UMI tags, aligned these to the mm10 transcriptome using STAR (v.2.5.1b) and reported cell-specific gene expression count estimates.
All subsequent analyses were performed in R v.3.6.0 using the Seurat (v3) package.  Genes were considered to be ‘expressed’ if the estimated (log10) count was at least 0.1. Primary filtering was then performed by removing from consideration: cells expressing fewer than 50 genes and cells for which mitochondrial genes made up greater than 10% of all expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text containing raw counts

extract_protocol:
Pituitaries were harvested, the posterior and the anterior lobes were removed and intermediate lobes isolated and incubated separately in a solution of papain  for 15 min at 37ºC in presence of 10ug/ml of both DNAse  and Rock Inhibitor. The papain solution was then removed, and mechanical dissociation was performed on ice in pituisphere medium.
Library generation for 10x Genomics analysis were performed following the Chromium Single Cell 3′ Reagents Kits (10x Genomics) and sequenced on an Hiseq4000 (Illumina).

treatment_protocol: Tamoxifen administration by oral gavage in 4-week old mice

value: 3-month old

value: Pituitary gland


title: p27null.1


title: WT


title: P27NULL


title: Single Dorsal root ganglion neuron_SNI 14d [S696]

description:
S696
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S697]

description:
S697
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: p27nullSOX.1


title: p27nullSOX.2


title: Single Dorsal root ganglion neuron_SNI 14d [S714]

description:
S714
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: p27nullSOX.3


title: Single Dorsal root ganglion neuron_SNI 14d [S694]

description:
S694
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: p27null_2_months.2

value: 2-month old


title: Single Dorsal root ganglion neuron_SNI 14d [S689]

description:
S689
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S693]

description:
S693
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: p27wt_2months.3


title: p27null_2_months.1


title: Single Dorsal root ganglion neuron_SNI 14d [S698]

description:
S698
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: p27wt_2months.1


title: p27null_7months.1

value: 7-month old


title: Single Dorsal root ganglion neuron_SNI 14d [S686]

description:
S686
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: p27null_7months.2


title: p27wt_2months.2


title: p27null_7months.3


title: Single Dorsal root ganglion neuron_SNI 14d [S683]

description:
S683
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: VitD_VEH_C

city: Stuttgart

first: Cristiana

last: Lungu

state: BW

address: Allmandring 31

department: Institute of Cell Biology and Immunology

country: Germany

institute: University of Stuttgart

data_processing:
The FASTQ  files were mapped to the mouse mm9 genome using TopHat Gapped-read mapper for RNA-seq data with very-sensitive BOWTIE2 settings. The differential analysis was performed by using Cuffdiff with default settings.
Genome_build: mm9
Supplementary_files_format_and_content: The provided mRNA-Seq analysis files present the differentially regulated genes between the indicated conditions in excel file format.

growth_protocol: Mouse calvarial osteoblasts were maintained in aMEM complete media with 10% FBS and 1% P/S

extract_protocol:
The total cell RNA was isolated with standard TRIzol extraction protocol
4 µg of total cell RNA was used for library preparation with NEXTflex Rapid Directional mRNA-Seq from Bioo Scientific and 500ng of total cell RNA was used for library preparation with TruSeq RNA Smaple Prep Kit-v2 following manufacturers' protocols.

treatment_protocol: For induction of RNF40 knockout, the cells were treated with 250nM of 4-hydroxytamoxifen or equivalent volume of vehicle (ethanol). For differentiation, cells were treated with 5 mM β-glycerophosphate and 0.2 mM ascorbate. For vitamin D studies, cells were treated for 7 days with 10nM calcitriol or equal volume of vehicle (DMSO).

tag: strain background

tag: genotype/variation

value: Mutant RNF40RosaCreERT2 mouse

value: Primary Calvarial Osteoblasts

value: for 7 d with vehicle(ethanol), and then  for additional 7 days with  10nM calcitriol

tag: library prep kit

value: TruSeq RNA Smaple Prep Kit-v2, Illumina


title: Single Dorsal root ganglion neuron_SNI 14d [S684]

description:
S684
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

value: Single Dorsal root ganglion neuron


title: VitD_Veh_B


title: p27wt_7months.1


title: Single Dorsal root ganglion neuron_SNI 14d [S682]

description:
S682
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S675]

description:
S675
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S676]

description:
S676
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S677]

description:
S677
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: p27wt_7months.2


title: VitD_Veh_A


title: VitD_TAM_C

value: for 7 d with 250nM 4-hydroxytamoxifen, and then  for additional 7 days with  10nM calcitriol


title: CT 2

value: liver


title: Single Dorsal root ganglion neuron_SNI 14d [S673]

description:
S673
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

value: SNI 14d


title: Single Dorsal root ganglion neuron_SNI 14d [S674]

description:
S674
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S685]

description:
S685
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S687]

description:
S687
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S671]

description:
S671
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S678]

description:
S678
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: VitD_TAM_B


title: DMSO_VEH_C

value: for 7 d with vehicle(ethanol), and then  for additional 7 days with  DMSO


title: DMSO_VEH_A


title: VitD_TAM_A


title: DMSO_VEH_B


title: Single Dorsal root ganglion neuron_SNI 14d [S657]

description:
S657
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: DMSO_TAM_C

value: for 7 d with 250nM 4-hydroxytamoxifen, and then  for additional 7 days with  DMSO


title: Single Dorsal root ganglion neuron_SNI 14d [S656]

description:
S656
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S655]

description:
S655
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: DMSO_TAM_B


title: Single Dorsal root ganglion neuron_SNI 14d [S649]

description:
S649
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S650]

description:
S650
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: VitD_VEH_H2Bub1_B

data_processing:
The FASTQ files were mapped to the mouse reference genome (assembly mm9) using BOWTIE2 with very-sensitive presets in end-to-end mode. The resulting BAM files of ChIPs were deduplicated and MAPQ >2 filtered using Samtools. The corresponding BAM files of the replicates were merged within condition. The merged BAM files were normalized to 1x genomic content (RPGC) using the bamCoverage function of Deeptools.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig represent the normalized reads per genomic content (RPGC) values of ChIP-seq signal

extract_protocol:
The ChIP was performed with 20 min crosslinking in 1 % formaldehyde in PBS. 1µg antibody was used for immunoprecipitation. After reversing the cross-linking, the DNA was isolated by phenol-chloroform-isoamyl extraction.
Libraries were prepared with MicroPlex Library Preparation Kit following the manufacturer's instructions

value: for 7 d with vehicle(ethanol) and then  for additional 7 days with 10nM calcitriol

tag: chip antibody

value: H2Bub1 (D11), Cell Signaling #5546

tag: molecule subtype

value: ChIP DNA


title: DMSO_VEH_H2Bub1_B

value: for 7 d with vehicle (ethanol) and then  for additional 7 days with DMSO


title: VitD_VEH_H2Bub1_A


title: Single Dorsal root ganglion neuron_Control [S740]

description:
S740
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

value: Control


title: DMSO_TAM_A


title: DMSO_VEH_H2Bub1_A


title: Single Dorsal root ganglion neuron_SNI 14d [S647]

description:
S647
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S643]

description:
S643
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: VitD_VEH_H3K4me3_B

value: H3K4me3, Diagenode C15410003


title: Single Dorsal root ganglion neuron_SNI 14d [S642]

description:
S642
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: VitD_VEH_H3K4me3_A


title: Single Dorsal root ganglion neuron_SNI 14d [S641]

description:
S641
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S645]

description:
S645
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S660]

description:
S660
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S639]

description:
S639
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: VitD_TAM_H3K4me3_B

value: for 7 d with 250nM 4-hydroxytamoxifen, and then  for additional 7 days with 10nM calcitriol


title: Single Dorsal root ganglion neuron_SNI 14d [S654]

description:
S654
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S638]

description:
S638
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: VitD_TAM_H3K4me3_A

value: Mutant RNF40RosaCreERT2 mouse


title: DMSO_VEH_H3K4me3_A

value: Primary Calvarial Osteoblasts


title: Single Dorsal root ganglion neuron_SNI 14d [S640]

description:
S640
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S634]

description:
S634
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S635]

description:
S635
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: DMSO_TAM_H3K4me3_A


title: DMSO_VEH_H3K4me3_B


title: Single Dorsal root ganglion neuron_SNI 14d [S632]

description:
S632
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S619]

description:
S619
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Human 2 - Strain+Treatment

city: Tucson

first: Kellen

last: Chen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

data_processing:
Base calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation of mkfastq
Then aligned against the GRCh38 v3.0.0 (human) genome using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample
Cell barcodes representative of quality cells were delineated from barcodes of apoptotic cells or background RNA based on a threshold of having at least 200 unique transcripts profiled, less than 10,000 total transcripts, and less than 10% of their transcriptome of mitochondrial origin.
Unique molecular identifiers (UMIs) from each cell barcode were retained for all downstream analysis.
Raw UMI counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1).
Highly variable genes were identified, and cells were scaled by regression to the fraction of mitochondrial transcripts. Aggregated data was then evaluated using uniform manifold approximation and projection (UMAP) analysis
Genome_build: GRCh38 v3.0.0 (human)
Supplementary_files_format_and_content: barcodes.tsv.gz  features.tsv.gz  matrix.mtx.gz

source_name: Dermal Fibroblasts

growth_protocol: Human skin samples were obtained under the approved IRB (#54225) and collected from three surgical procedures, fibroblasts were cultured and grown. Fibroblasts were then cultured in a 3D collagen scaffold system for 48 hours to either mechanically strain the cells or also treat with focal adhesion kinase inhibitor (FAKI)

extract_protocol:
This cellular suspension was then submitted for droplet-based microfluidic single cell RNA sequencing (scRNA-seq) at the Stanford Functional Genomics Facility (SFGF) using the 10x Chromium Single Cell platform (Single Cell 3’ v3, 10x Genomics, USA).
cDNA was fragmented followed by end repair and A-tailing at 65°C for 30min. cDNA were double-sided size selected using SpriSelect beats. Sequencing adaptors were ligated to the cDNA at 20°C for 15min. cDNA was amplified using a sample-specific index oligo as primer, followed by another round of double-sided size selection using SpriSelect beads.
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA libraries were sequenced on a HiSeq 4000 Illumina platform aiming for 50,000 reads per cell.

treatment_protocol: 48 hours of 10% strain, or strain + 10uM FAKI

tag: individual

value: Human 2

tag: passages

value: second to third passage

value: skin

value: Dermal Fibroblasts

value: Strain+Treatment


title: Human 2 - Strain v1

tag: cell type

value: Strain v1


title: Single Dorsal root ganglion neuron_SNI 14d [S618]

description:
S618
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

value: SNI 14d

value: Single Dorsal root ganglion neuron


title: Human 2 - Strain repeat

tag: tissue

value: Strain repeat


title: Single Dorsal root ganglion neuron_SNI 14d [S633]

description:
S633
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S616]

description:
S616
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S598]

description:
S598
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Human 2 - No Strain (Control)

value: No Strain (Control)


title: Single Dorsal root ganglion neuron_SNI 14d [S596]

description:
S596
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S617]

description:
S617
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Human 3 - tagged with hash-seq antibodies for No Strain, Strain, Treatment, and No Strain + Treatment

description:
K02 (or H3_Hash)
20191107_UHTS_Kellen_Chen_KC02_pool_submission_v4.xlsx contains the information for how to deconvolute the hashing antibody information for the KC02 sample.

value: Human 3


title: Single Dorsal root ganglion neuron_SNI 14d [S599]

description:
S599
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S595]

description:
S595
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S597]

description:
S597
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Human 1 - Strain+Treatment

description: KC-T

value: Human 1


title: Single Dorsal root ganglion neuron_SNI 14d [S594]

description:
S594
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: DMSO_TAM_H3K4me3_B

value: for 7 d with 250nM 4-hydroxytamoxifen, and then  for additional 7 days with DMSO

value: ChIP DNA


title: Human 1 - Strain

description: KC-S

value: Strain


title: RNASeq of homo sapiens: mono-cultured isogenic KO microglia (28_Mi_C17_Mo)

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

description: differentiation 3

data_processing:
Basecalling and sample de-multiplexing was performed with bcl2fastq v2.17.1.14 and default parameters
Reads were quality check with fastqc default parameters
Reads for each sample/replicate were mapped against the mouse genome assembly using STAR read aligner v2.5.2a
RefSeq annotated genes were quantified with samtools v1.5 and in-house scripts
Genome_build: hg38
Supplementary_files_format_and_content: Read counts per gene

source_name: microglia

extract_protocol:
Cells were lysed and the RNA purified using the High Pure RNA Isolation Kit from Roche following the provided protocol. RNA purity was assessed using the Agilent 2100 Bioanalyzer.
Strand-specific mRNA-seq libraries were generated from 1 ug total RNA using the TruSeq Stranded mRNA library prep kit (Illumina) according to manufacturer's instructions

tag: isolate

value: BIONi010-C-17 iPSC line deposited at EBISC

tag: Sex

value: male

value: isogenic KO

tag: karyotype


title: Human 1 - No Strain (Control)

description: KC-C

value: second to third passage

tag: treatment


title: RNASeq of homo sapiens: mono-cultured isogenic KO microglia (30_Mi_C17_Mo)

description: differentiation 5

tag: age


title: RNASeq of homo sapiens: mono-cultured isogenic KO microglia (29_Mi_C17_Mo)

description: differentiation 4


title: Single Dorsal root ganglion neuron_SNI 14d [S593]

description:
S593
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

tag: strain

tag: tissue/cell type

tag: technology


title: Single Dorsal root ganglion neuron_SNI 14d [S591]

description:
S591
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S592]

description:
S592
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S590]

description:
S590
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S589]

description:
S589
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: RNASeq of homo sapiens: mono-cultured isogenic KO microglia (27_Mi_C17_Mo)

description: differentiation 2


title: RNASeq of homo sapiens: mono-cultured isogenic KO microglia (26_Mi_C17_Mo)

description: differentiation 1


title: Single Dorsal root ganglion neuron_SNI 14d [S588]

description:
S588
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S587]

description:
S587
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: RNASeq of homo sapiens: mono-cultured wt microglia (25_Mi_WT_Mo)

description: differentiation 5

value: BIONi010-C iPSC line deposited at EBISC

value: normal


title: RNASeq of homo sapiens: mono-cultured wt microglia (23_Mi_WT_Mo)

description: differentiation 3


title: RNASeq of homo sapiens: mono-cultured wt microglia (21_Mi_WT_Mo)

description: differentiation 1


title: Single Dorsal root ganglion neuron_SNI 14d [S586]

description:
S586
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: RNASeq of homo sapiens: mono-cultured wt microglia (22_Mi_WT_Mo)

description: differentiation 2


title: RNASeq of homo sapiens: co-cultured wt microglia (15_Mi_WT_Co)

description: differentiation 5


title: Single Dorsal root ganglion neuron_SNI 14d [S585]

description:
S585
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S583]

description:
S583
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: RNASeq of homo sapiens: co-cultured wt microglia (13_Mi_WT_Co)

description: differentiation 3


title: Single Dorsal root ganglion neuron_SNI 14d [S581]

description:
S581
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S584]

description:
S584
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [s422]

description:
s422
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [s497]

description:
s497
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: RNASeq of homo sapiens: co-cultured wt microglia (14_Mi_WT_Co)

description: differentiation 4


title: Single Dorsal root ganglion neuron_SNI 14d [s371]

description:
s371
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: RNASeq of homo sapiens: co-cultured wt microglia (12_Mi_WT_Co)

description: differentiation 2


title: RNASeq of homo sapiens: co-cultured wt microglia (11_Mi_WT_Co)

description: differentiation 1


title: RNASeq of homo sapiens: macrophage precursor (05_Mo_WT_Ctrl)

description: differentiation 5

source_name: macrophage precursor


title: Single Dorsal root ganglion neuron_SNI 14d [S339]

description:
S339
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: RNASeq of homo sapiens: macrophage precursor (04_Mo_WT_Ctrl)

description: differentiation 4


title: Single Dorsal root ganglion neuron_SNI 14d [S346]

description:
S346
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: RNASeq of homo sapiens: mono-cultured wt microglia (24_Mi_WT_Mo)

description: differentiation 4


title: RNASeq of homo sapiens: macrophage precursor (01_Mo_WT_Ctrl)

description: differentiation 1


title: RNASeq of homo sapiens: macrophage precursor (02_Mo_WT_Ctrl)

description: differentiation 2


title: Single Dorsal root ganglion neuron_SNI 14d [s294]

description:
s294
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: K562 DRIPc WT LS60B rep2

city: Davis

first: Frederic

last: Chedin

address: 1 Shields Avenue

department: MCB

institute: UC Davis

data_processing:
Library strategy: DRIPc-seq
Raw fastq reads were trimmed with fastq-mcf v2.4.4 and mapped with STAR v2.7. Mapped reads were duplicate-removed using samtools.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30)

source_name: K562 cells

extract_protocol:
Standard illumina protocol.
DRIP-seq and DRIPc-seq were performed as described in Sanz et al, 2016. Briefly, for DRIP-seq, genomic DNA was extracted from HeLa and K562 cell lines and fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI. Monoclonal S9.6 antibody was used to enrich for RNA/DNA hybrid and RNA was removed using RNase H before being subjected to standard Illumina library construction protocol. For DRIPc-seq, enriched R-loop fragments were further subjected to DNase I treatment and the remaining RNA was subjected to second strand synthesis using dUTP instead of dTTP for strand-specific library construction. Illumina TruSeq Single adapter was ligated and the cDNA and amplified as per standard Illumina TruSeq Single end protocol.

treatment_protocol: DRIPc-seq samples were treated with or without RNase H

tag: cell line

value: bone marrow CML cells

value: control


title: Single Dorsal root ganglion neuron_SNI 14d [S275]

description:
S275
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

value: SNI 14d


title: Single Dorsal root ganglion neuron_SNI 14d [S279]

description:
S279
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

value: Single Dorsal root ganglion neuron


title: Single Dorsal root ganglion neuron_SNI 14d [S274]

description:
S274
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S276]

description:
S276
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: K562 DRIPc WT LS60A rep1


title: Single Dorsal root ganglion neuron_SNI 14d [S273]

description:
S273
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S272]

description:
S272
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: HeLa DRIPc WT LS61C rep2

source_name: HeLa cells

value: HeLa

value: cervical cancer cells


title: HeLa DRIPc WT LS61H rep3


title: HeLa DRIPc WT LS61A rep1


title: Single Dorsal root ganglion neuron_SNI 14d [S271]

description:
S271
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S260]

description:
S260
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S257]

description:
S257
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S256]

description:
S256
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S258]

description:
S258
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: RNASeq of homo sapiens: macrophage precursor (03_Mo_WT_Ctrl)

description: differentiation 3


title: Single Dorsal root ganglion neuron_SNI 14d [S255]

description:
S255
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S254]

description:
S254
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S253]

description:
S253
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject0022

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description:
Pre TW19610 Sub022
UPN119 cells stimulated with PRE Sub0022 plasma

hyb_protocol: The Affymetrix GeneChip Human Genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through Paired TTest function in Partek GS.

source_name: UPN119 cells stimulated with pre-Lp299v supplementation plasma in men with stable CAD

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN119 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of plasma samples obtained prior to and immediately following 6 weeks of Lp299v supplementation from 19 men with stable CAD.  Cultures were prepared in Costar 24-well plates (Cellular Technology LTD) using 500,000 cells/well and in RPMI 1,640 medium supplemented with 100 U/ml penicillin and 100 ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cells

value: UPN119 cells

value: stimulated with PRE Sub0022 plasma


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject0021

description:
Post TW19610 Sub021
UPN119 cells stimulated with POST Sub0021 plasma

source_name: UPN119 cells stimulated with post-Lp299v supplementation plasma in men with stable CAD

value: stimulated with POST Sub0021 plasma


title: Single Dorsal root ganglion neuron_SNI 14d [S252]

description:
S252
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S250]

description:
S250
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S247]

description:
S247
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S245]

description:
S245
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S246]

description:
S246
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S241]

description:
S241
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S228]

description:
S228
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S226]

description:
S226
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject0020

description:
Post TW19610 Sub020
UPN119 cells stimulated with POST Sub0020 plasma

value: stimulated with POST Sub0020 plasma


title: Single Dorsal root ganglion neuron_SNI 14d [S225]

description:
S225
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject0022

description:
Post TW19610 Sub022
UPN119 cells stimulated with POST Sub0022 plasma

value: stimulated with POST Sub0022 plasma


title: Single Dorsal root ganglion neuron_SNI 14d [S251]

description:
S251
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S249]

description:
S249
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S224]

description:
S224
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject0021

description:
Pre TW19610 Sub021
UPN119 cells stimulated with PRE Sub0021 plasma

value: stimulated with PRE Sub0021 plasma


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject0017

description:
Post TW19610 Sub017
UPN119 cells stimulated with POST Sub0017 plasma

value: stimulated with POST Sub0017 plasma


title: Single Dorsal root ganglion neuron_SNI 14d [S223]

description:
S223
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject0018

description:
Post TW19610 Sub018
UPN119 cells stimulated with POST Sub0018 plasma

value: stimulated with POST Sub0018 plasma


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject0016

description:
Pre TW19610 Sub016
UPN119 cells stimulated with PRE Sub0016 plasma

value: stimulated with PRE Sub0016 plasma


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject0019

description:
Pre TW19610 Sub019
UPN119 cells stimulated with PRE Sub0019 plasma

value: stimulated with PRE Sub0019 plasma


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject0013

description:
Pre TW19610 Sub013
UPN119 cells stimulated with PRE Sub0013 plasma

value: stimulated with PRE Sub0013 plasma


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject0017

description:
Pre TW19610 Sub017
UPN119 cells stimulated with PRE Sub0017 plasma

value: stimulated with PRE Sub0017 plasma


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject0018

description:
Pre TW19610 Sub018
UPN119 cells stimulated with PRE Sub0018 plasma

value: stimulated with PRE Sub0018 plasma


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject0014

description:
Post TW19610 Sub014
UPN119 cells stimulated with POST Sub0014 plasma

value: stimulated with POST Sub0014 plasma


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject0020

description:
Pre TW19610 Sub020
UPN119 cells stimulated with PRE Sub0020 plasma

value: stimulated with PRE Sub0020 plasma


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject0013

description:
Post TW19610 Sub013
UPN119 cells stimulated with POST Sub0013 plasma

value: stimulated with POST Sub0013 plasma


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject0019

description:
Post TW19610 Sub019
UPN119 cells stimulated with POST Sub0019 plasma

value: stimulated with POST Sub0019 plasma


title: Single Dorsal root ganglion neuron_SNI 14d [S220]

description:
S220
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

value: SNI 14d

value: Single Dorsal root ganglion neuron


title: Single Dorsal root ganglion neuron_SNI 14d [S219]

description:
S219
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject0011

description:
Pre TW19610 Sub011
UPN119 cells stimulated with PRE Sub0011plasma

value: UPN119 cells

value: stimulated with PRE Sub0011plasma


title: Single Dorsal root ganglion neuron_SNI 14d [S216]

description:
S216
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S215]

description:
S215
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject0011

description:
Post TW19610 Sub011
UPN119 cells stimulated with POST Sub0011 plasma

value: stimulated with POST Sub0011 plasma


title: Single Dorsal root ganglion neuron_SNI 14d [S217]

description:
S217
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject0010

description:
Post TW19610 Sub010 DAI
UPN119 cells stimulated with POST Sub0010 plasma

source_name: UPN119 cells stimulated with post-Lp299v supplementation plasma in men with stable CAD with daily alcohol intake (DAI)

value: stimulated with POST Sub0010 plasma


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject0016

description:
Post TW19610 Sub016
UPN119 cells stimulated with POST Sub0016 plasma

value: stimulated with POST Sub0016 plasma


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject009

description:
Post TW19610 Sub009
UPN119 cells stimulated with POST Sub009 plasma

value: stimulated with POST Sub009 plasma


title: Single Dorsal root ganglion neuron_SNI 14d [S222]

description:
S222
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S214]

description:
S214
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject0010

description:
Pre TW19610 Sub010 DAI
UPN119 cells stimulated with PRE Sub0010 plasma

source_name: UPN119 cells stimulated with pre-Lp299v supplementation plasma in men with stable CAD with daily alcohol intake (DAI)

value: stimulated with PRE Sub0010 plasma


title: Single Dorsal root ganglion neuron_SNI 14d [S221]

description:
S221
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S213]

description:
S213
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S212]

description:
S212
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S210]

description:
S210
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S211]

description:
S211
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject007

description:
Pre TW19610 Sub007
UPN119 cells stimulated with PRE Sub007 plasma

value: stimulated with PRE Sub007 plasma


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject009

description:
Pre TW19610 Sub009
UPN119 cells stimulated with PRE Sub009 plasma

value: stimulated with PRE Sub009 plasma


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject008

description:
Post TW19610 Sub008 DAI
UPN119 cells stimulated with POST Sub008 plasma

value: stimulated with POST Sub008 plasma


title: Single Dorsal root ganglion neuron_SNI 14d [S209]

description:
S209
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S208]

description:
S208
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S205]

description:
S205
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject005

description:
Post TW19610 Sub005 DAI
UPN119 cells stimulated with POST Sub005 plasma

value: stimulated with POST Sub005 plasma


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject005

description:
Pre TW19610 Sub005 DAI
UPN119 cells stimulated with PRE Sub005 plasma

value: stimulated with PRE Sub005 plasma


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject006

description:
Pre TW19610 Sub006
UPN119 cells stimulated with PRE Sub006 plasma

value: stimulated with PRE Sub006 plasma


title: Single Dorsal root ganglion neuron_SNI 14d [S202]

description:
S202
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S203]

description:
S203
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject004

description:
Post TW19610 Sub004
UPN119 cells stimulated with POST Sub004 plasma

value: stimulated with POST Sub004 plasma


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject008

description:
Pre TW19610 Sub008 DAI
UPN119 cells stimulated with PRE Sub008 plasma

value: stimulated with PRE Sub008 plasma


title: Single Dorsal root ganglion neuron_SNI 14d [S199]

description:
S199
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

value: SNI 14d


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject004

description:
Pre TW19610 Sub004
UPN119 cells stimulated with PRE Sub004 plasma

value: stimulated with PRE Sub004 plasma


title: Single Dorsal root ganglion neuron_SNI 14d [S201]

description:
S201
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

value: Single Dorsal root ganglion neuron


title: Single Dorsal root ganglion neuron_SNI 14d [S197]

description:
S197
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S195]

description:
S195
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S196]

description:
S196
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S192]

description:
S192
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S194]

description:
S194
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject001

description:
Post TW19610 Sub001 DAI
UPN119 cells stimulated with POST Sub001 plasma

value: UPN119 cells

value: stimulated with POST Sub001 plasma


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject007

description:
Post TW19610 Sub007
UPN119 cells stimulated with POST Sub007 plasma

value: stimulated with POST Sub007 plasma


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject003

description:
Post TW19610 Sub003
UPN119 cells stimulated with POST Sub003 plasma

value: stimulated with POST Sub003 plasma


title: UPN119 Cells Exposed to Post-Lp299v Supplementation Plasma - Subject006

description:
Post TW19610 Sub006
UPN119 cells stimulated with POST Sub006 plasma

value: stimulated with POST Sub006 plasma


title: 100 mg Recovery B47668

city: Foster City

first: Ricardo

last: Ramirez

address: 333 Lakeside Drive

institute: Gilead Sciences, Inc.

description: 100 mg Recovery

data_processing:
Basecalls from Illumina samples were performed using CASAVA
Reads were aligned to mouse genome assembly rn5 using STAR 2.4
Genes were quantified using RSEM
Genome_build: rn5
Supplementary_files_format_and_content: gene counts matrix

organism: Rattus norvegicus

source_name: liver (left lateral lobe)

extract_protocol:
RNA samples were converted into cDNA libraries using the Illumina TruSeq  Stranded mRNA sample preparation kit (Illumina # RS-122-2103).
Libraries were prepared for sequencing using the Ampliseq human transcriptome kit (Thermo) for sequencing on Ion Torrent

treatment_protocol: Male Wistar Han rats (n = 3 per dose group) were dosed p.o. once daily for seven days with GS-5801 at 10, 30, or 100 mg/kg and sacrificed 24 hours after the last dose. A second group of male Wistar Han rats (n = 3 per dose group) were dosed p.o. once daily for seven days with GS-5801 at 10, 30, or 100 mg/kg and taken off drug for seven days before animals were sacrificed. At sacrifice, approximately 100 mg samples of liver tissue (left lateral lobe) were collected, snap frozen using liquid nitrogen, and stored at -80 °C for transcriptome analysis by RNAseq.

tag: timepoint

value: Recovery


title: 100 mg Recovery B47669

description: 100 mg Recovery


title: 100 mg Recovery B47667

description: 100 mg Recovery


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject003

description:
Pre TW19610 Sub003
UPN119 cells stimulated with PRE Sub003 plasma

value: stimulated with PRE Sub003 plasma


title: 100 mg Terminal B47673

description: 100 mg Terminal

value: Terminal


title: Single Dorsal root ganglion neuron_SNI 14d [S191]

description:
S191
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 100 mg Terminal B47674

description: 100 mg Terminal


title: UPN119 Cells Exposed to Pre-Lp299v Supplementation Plasma - Subject001

description:
Pre TW19610 Sub001 DAI
UPN119 cells stimulated with PRE Sub001 plasma

value: stimulated with PRE Sub001 plasma


title: 30 mg Recovery B47653

description: 30 mg Recovery

value: 30 mg


title: 30 mg Recovery B47652

description: 30 mg Recovery


title: Single Dorsal root ganglion neuron_SNI 14d [S188]

description:
S188
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S190]

description:
S190
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S181]

description:
S181
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S187]

description:
S187
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 30 mg Recovery B47651

description: 30 mg Recovery


title: 30 mg Terminal B47659

description: 30 mg Terminal


title: Single Dorsal root ganglion neuron_SNI 14d [S186]

description:
S186
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 30 mg Terminal B47657

description: 30 mg Terminal


title: 100 mg Terminal B47675

description: 100 mg Terminal


title: 10 mg Recovery B47637

description: 10 mg Recovery

value: 10 mg


title: Single Dorsal root ganglion neuron_SNI 14d [S177]

description:
S177
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S176]

description:
S176
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S174]

description:
S174
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 10 mg Recovery B47635

description: 10 mg Recovery


title: Single Dorsal root ganglion neuron_SNI 14d [S173]

description:
S173
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S171]

description:
S171
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: 10 mg Terminal B47643

description: 10 mg Terminal


title: 10 mg Terminal B47641

description: 10 mg Terminal


title: Single Dorsal root ganglion neuron_SNI 14d [S168]

description:
S168
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Vehicle Recovery Sacrifice B47607

description: Vehicle Recovery Sacrifice

value: Vehicle


title: Single Dorsal root ganglion neuron_SNI 14d [S167]

description:
S167
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Vehicle Recovery Sacrifice B47606

description: Vehicle Recovery Sacrifice


title: Vehicle Recovery Sacrifice B47608

description: Vehicle Recovery Sacrifice


title: 30 mg Terminal B47658

description: 30 mg Terminal


title: Single Dorsal root ganglion neuron_SNI 14d [S166]

description:
S166
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S280]

description:
S280
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Vehicle Terminal Sacrifice B47611

description: Vehicle Terminal Sacrifice


title: Single Dorsal root ganglion neuron_SNI 14d [S179]

description:
S179
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S164]

description:
S164
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S162]

description:
S162
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Vehicle Terminal Sacrifice B47609

description: Vehicle Terminal Sacrifice


title: Vehicle Terminal Sacrifice B47610

description: Vehicle Terminal Sacrifice


title: H30_mid-secretory phase

city: Daejeon

first: Seong-Lan

last: Yu

address: Gasuwon-dong

department: Myunggok Medical Research Institute

country: South Korea

institute: Konyang university

description: mid-secretory phase of the endometrium

data_processing:
Raw data were normalized using the relative log expression method in DESeq2
Relative gene abundance was measured in FPKM using StringTie.

source_name: endometrium

extract_protocol:
Total RNA was isolated from endometrial tissue immediately after biopsy using TRIzol reagent according to the manufacturer’s instructions.
Ten nanograms of RNA isolated from each sample was used to construct miRNA sequencing libraries using a SMARTer small noncoding RNA (smRNA)-Seq Kit according to the manufacturer's instructions.

value: endometrium


title: 10 mg Recovery B47636

description: 10 mg Recovery


title: H29_proliferative phase

description: proliferatvie phase of the endometrium


title: 10 mg Terminal B47642

description: 10 mg Terminal


title: Single Dorsal root ganglion neuron_SNI 14d [S159]

description:
S159
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S156]

description:
S156
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S169]

description:
S169
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: H25_proliferative phase

description: proliferatvie phase of the endometrium


title: H23_proliferative phase

description: proliferatvie phase of the endometrium


title: Single Dorsal root ganglion neuron_SNI 14d [S148]

description:
S148
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: H10_proliferative phase

description: proliferatvie phase of the endometrium


title: H4_mid-secretory phase

description: mid-secretory phase of the endometrium


title: Single Dorsal root ganglion neuron_SNI 14d [S147]

description:
S147
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: H2_mid-secretory phase

description: mid-secretory phase of the endometrium


title: Single Dorsal root ganglion neuron_SNI 14d [S146]

description:
S146
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S142]

description:
S142
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S143]

description:
S143
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S144]

description:
S144
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S141]

description:
S141
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S140]

description:
S140
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S145]

description:
S145
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_4hr_PBS_MYB_rep1

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human assembly hg19 using bowtie2 (v2.2.2) with default parameters and duplicates were collapsed using Picard (v2.16).
To create density files, read overlap density was calculated with an extension of 200 bp, the signal was then normalized to sequencing depth and converted to BigWig using BEDTools.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files containing read densities normalized to sequencing depth.

source_name: MV411 cell line

growth_protocol: MV411 cells were cultured at 37°C in 5% CO2 humidified atmosphere in RPMI medium supplemented with 10% fetal bovine serum (FBS), antibiotics (100 U/mL penicillin, 100 mg/mL streptomycin), and L-glutamine (1%).

extract_protocol: ChIP-seq libraries were constructed with the NEBNext ChIP-seq library prep kit following the manufacturer’s recommended protocol (New England Biolabs, Ipswich, MA, USA).

treatment_protocol: MV411 cells were resuspended to a concentration of 15 million cells/5 mL of working media. Peptide suspensions were made in PBS of CREBMIM and CRYBMIM peptides from lyophilized product. Peptide suspensions or PBS control were added directly to working media to a final concentration of 20 µM. Cells were incubated with peptide or control for 1h or 4h at 37°C and then resuspended in PBS.

value: MV411 leukemia cell line

value: PBS control

tag: time

value: 4 hr

tag: chip antibody

value: Abcam ab45150 Anti-v-Myb and c-Myb, rabbit monoclonal, Clone #EP769Y, lot # GR246427-10


title: MV411_4hr_PBS_CREB_rep2

value: EMD Millipore 17-600 Anti-CREB, rabbit monoclonal, Clone # NL904


title: MV411_4hr_PBS_MYB_rep2


title: MV411_4hr_PBS_Input_rep1


title: MV411_4hr_PBS_CREB_rep3


title: MV411_4hr_PBS_MYB_rep3


title: Single Dorsal root ganglion neuron_SNI 14d [S139]

description:
S139
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt

value: SNI 14d

value: Single Dorsal root ganglion neuron


title: MV411_4hr_PBS_CREB_rep1


title: Single Dorsal root ganglion neuron_SNI 14d [S138]

description:
S138
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S149]

description:
S149
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S161]

description:
S161
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S135]

description:
S135
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: Single Dorsal root ganglion neuron_SNI 14d [S136]

description:
S136
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_4hr_PBS_CBP_rep1

value: Cell Signaling  #7425 Anti-CBP, rabbit monoclonal, Clone D9B6, lot #1


title: Single Dorsal root ganglion neuron_SNI 14d [S134]

description:
S134
processed data file:
Smart-seq2_FPKM.txt
Smart-seq2_FPKM_metadata.txt


title: MV411_4hr_PBS_CBP_rep3