title: WT-HiC-seq

value: WT


title: Patient 7871_Benign Basal

status: Public on Dec 03 2019

type: SRA

city: Durham

first: Yanjing

last: Li

state: NC

address: 905 S. LaSalle Street GSRB1, 3038

department: Pathology

country: USA

institute: Duke University

description:
DifferentialExpression-patients' samples
7871_BB

library_source: transcriptomic

data_processing:
RNA-seq data was processed using the TrimGalore toolkit, which employs Cutadapt to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads.  Only reads that were 20nt or longer after trimming were kept for further analysis
Reads were mapped to the GRCh37v75 version of the human genome and transcriptome (Kersey et al., 2012) using the STAR RNA-seq alignment tool (Dobin et al., 2013)
Gene counts were compiled using the HTSeq tool.  Only genes that had at least 10 reads in any given library were used in subsequent analysis
Normalization and differential expression was carried out using the DESeq2 (Love et al., 2014) Bioconductor (Huber et al., 2015) package with the R statistical programming environment.
Gene set enrichment analysis (Mootha et al., 2003) was performed to identify differentially regulated pathways and gene ontology terms for each of the comparisons performed.
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Patients' fresh prostate tissue

extract_protocol:
Fresh prostate tumor samples were obtained from patients with localized prostate adenocarcinoma who received prostatectomy and will be digested into single cells and sorted into Trop2+ CXCR2+ NE, Trop2+ CXCR2- luminal populations. Benign prostate tissue will be digested and sorted into Trop2+CXCR2-CD49f+ basal population. RNA was harvested using Trizol reagent. Illumina TruSeq stranded mRNA Sample Prep Kit was used to isolate mRNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: benign prostate tissue

tag: tumor stage

value: benign tissue

tag: cell type

value: Basal cells


title: Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, stressed 1708

status: Public on Dec 02 2019

city: New York

first: Laura

last: Kus

state: NY

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

description:
Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, stressed
Ribosomal-bound RNA
1708_Aldh1l1_TRAP_JD130_NAC_stressed_IP_Rep2

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

molecule: total RNA

organism: Mus musculus

source_name: Accumbens nucleus

growth_protocol: Not applicable

extract_protocol:
The prefrontal cortex, hippocampus, accumbens nucleus and caudate putamen were dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: Aldh1l1-TRAP mice were kept together with the CD1 aggressive mouse in a large cage with the Plexiglas divider, that allows visual and olfactory, but no physical contact. The Aldh1l1-TRAP mouse was exposed to direct contact with the CD1 mouse for 10 minutes daily, for ten days. Control mice were kept group housed, 2-3 mice per cage, in the same room but without direct visual contact with the cages included in social defeat paradigm. Mice were kept in a 12-hour light-dark cycle, at room temperature and with water and food provided ad libitum.

tag: animal line

tag: application

value: RNA-seq

tag: sample type

value: Immunopurified (IP)


title: Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, resilient 1704

description:
Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, resilient
Ribosomal-bound RNA
1704_Aldh1l1_TRAP_JD130_NAC_resilient_IP_Rep1


title: Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, resilient 1706

description:
Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, resilient
Ribosomal-bound RNA
1706_Aldh1l1_TRAP_JD130_NAC_resilient_IP_Rep3


title: Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, stressed 1707

description:
Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, stressed
Ribosomal-bound RNA
1707_Aldh1l1_TRAP_JD130_NAC_stressed_IP_Rep1


title: Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, resilient 1705

description:
Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, resilient
Ribosomal-bound RNA
1705_Aldh1l1_TRAP_JD130_NAC_resilient_IP_Rep2


title: Patient 6953_Cancer Trop2+CXCR2- luminal

description:
DifferentialExpression-patients' samples
6953_CL

source_name: Patients' fresh prostate cancer tissue

value: prostate cancer

value: hormonal-sensitive primary prostate adenocarcinoma

value: Luminal cells


title: Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, control 1701

description:
Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, control
Ribosomal-bound RNA
1701_Aldh1l1_TRAP_JD130_NAC_control_IP_Rep1


title: Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, control 1703

description:
Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, control
Ribosomal-bound RNA
1703_Aldh1l1_TRAP_JD130_NAC_control_IP_Rep3


title: Aldh1l1-EGFP/Rpl10a (JD130), caudate putamen, control 1712

description:
Aldh1l1-EGFP/Rpl10a (JD130), caudate putamen, control
Ribosomal-bound RNA
1712_Aldh1l1_TRAP_JD130_CPU_control_IP_Rep2

source_name: Caudate putamen


title: Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, control 1702

description:
Aldh1l1-EGFP/Rpl10a (JD130), accumbens nucleus, control
Ribosomal-bound RNA
1702_Aldh1l1_TRAP_JD130_NAC_control_IP_Rep2


title: Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, stressed 1699

description:
Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, stressed
Ribosomal-bound RNA
1699_Aldh1l1_TRAP_JD130_HIP_stressed_IP_Rep4

source_name: Hippocampus


title: Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, control 1692

description:
Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, control
Ribosomal-bound RNA
1692_Aldh1l1_TRAP_JD130_HIP_control_IP_Rep3


title: Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, stressed 1697

description:
Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, stressed
Ribosomal-bound RNA
1697_Aldh1l1_TRAP_JD130_HIP_stressed_IP_Rep2


title: Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, resilient 1693

description:
Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, resilient
Ribosomal-bound RNA
1693_Aldh1l1_TRAP_JD130_HIP_resilient_IP_Rep1


title: Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, stressed 1696

description:
Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, stressed
Ribosomal-bound RNA
1696_Aldh1l1_TRAP_JD130_HIP_stressed_IP_Rep1


title: Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, resilient 1694

description:
Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, resilient
Ribosomal-bound RNA
1694_Aldh1l1_TRAP_JD130_HIP_resilient_IP_Rep2


title: Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, stressed 1698

description:
Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, stressed
Ribosomal-bound RNA
1698_Aldh1l1_TRAP_JD130_HIP_stressed_IP_Rep3


title: Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, stressed 1700

description:
Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, stressed
Ribosomal-bound RNA
1700_Aldh1l1_TRAP_JD130_HIP_stressed_IP_Rep5


title: Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, control 1691

description:
Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, control
Ribosomal-bound RNA
1691_Aldh1l1_TRAP_JD130_HIP_control_IP_Rep2


title: Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, stressed 1688

description:
Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, stressed
Ribosomal-bound RNA
1688_Aldh1l1_TRAP_JD130_PFC_stressed_IP_Rep4

source_name: Prefrontal cortex


title: Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, stressed 1686

description:
Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, stressed
Ribosomal-bound RNA
1686_Aldh1l1_TRAP_JD130_PFC_stressed_IP_Rep2


title: Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, control 1690

description:
Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, control
Ribosomal-bound RNA
1690_Aldh1l1_TRAP_JD130_HIP_control_IP_Rep1


title: Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, resilient 1695

description:
Aldh1l1-EGFP/Rpl10a (JD130), hippocampus, resilient
Ribosomal-bound RNA
1695_Aldh1l1_TRAP_JD130_HIP_resilient_IP_Rep3


title: SH-SY5Y, 0 hr, MOI=0.01, replicate 1

type: RNA

city: kunming

first: yongzhong

last: duan

state: Yunnan

address: chongrong west road, chenggong new district

country: China

institute: kunming medical university

description: miRNAs expression profile infected by HSV-1 in SH-SY5Y cells

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm

source_name: SH-SY5Y, 0 hr, MOI=0.01, replicate 1

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat #5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

growth_protocol: Human neuroblastoma cells SH-SY5Y and human glioblastoma cells U87MG were purchased from American Type Culture Collection (ATCC, VA, USA) and stored in Department of Viral Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences (Kunming, China). The above tow types of cells were cultured in Dulbecco′s modified Eagle′s medium (DMEM, Thermo Fisher Scientific, MA, USA), supplied with 10% (V/V) fetal bovine serum (FBS, Gibco, MA, USA) and penicillin–streptomycin (100 U/mL and 100 μg/mL). The cells were maintained at 37C in a humidified atmosphere containing 5% CO2.

extract_protocol: The total RNA of infected cells was extracted and purified using miRNeasy Mini Kit (QIAGEN, GmbH, Germany) according to the manufacturer’s instructions at the time point of 0, 4 and 10 hpi. The RNA concentration was measured by NanoDrop ND-2000 spectrophotometer (Thermo, MA, USA) and RNA integrity number (RIN) was determined by 2100 Bioanalyzer (Agilent technologies, CA, USA) and agarose gel electrophoresis.

treatment_protocol: SH-SY5Y and U87MG cells were seeded at a density of 3×105 cells/well in 12-well plate overnight to adhere. Cells were washed twice with phosphate buffer saline (PBS) and infected with HSV-1 strains of 17syn+、Kos and Mckrae at an MOI of 0.01, respectively.

tag: cell line


title: SH-SY5Y, 4 hr, MOI=0.01, replicate 1

source_name: SH-SY5Y, 4 hr, MOI=0.01, replicate 1


title: Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, stressed 1689

description:
Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, stressed
Ribosomal-bound RNA
1689_Aldh1l1_TRAP_JD130_PFC_stressed_IP_Rep5


title: Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, stressed 1687

description:
Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, stressed
Ribosomal-bound RNA
1687_Aldh1l1_TRAP_JD130_PFC_stressed_IP_Rep3


title: Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, stressed 1685

description:
Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, stressed
Ribosomal-bound RNA
1685_Aldh1l1_TRAP_JD130_PFC_stressed_IP_Rep1


title: Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, control 1680

description:
Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, control
Ribosomal-bound RNA
1680_Aldh1l1_TRAP_JD130_PFC_control_IP_Rep3


title: Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, control 1679

description:
Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, control
Ribosomal-bound RNA
1679_Aldh1l1_TRAP_JD130_PFC_control_IP_Rep2


title: Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, control 1678

description:
Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, control
Ribosomal-bound RNA
1678_Aldh1l1_TRAP_JD130_PFC_control_IP_Rep1


title: Mouse-Lin-Neg-CEBPA_V314VW+CSF3R_T618I-B

city: Portland

first: Theodore

middle: Paul

last: Braun

state: OR

address: 3181 SW Sam Jackson Park Road

department: Knight Cancer Institute

institute: OHSU

description: RNA-seq on marine bone marrow cells simultaneously transduced with CEBPA_V314VW and CSF3R_T618I vector

data_processing:
Raw reads were trimmed with Trimmmomatic and aligned to mm10 with STAR to generate gene count tables.
Gene count tables were analyzed using the Bioconductor Package DESeq2.
Raw p values were adjusted for multiple comparisons using the Benjamini-Hochberg method.
Genome_build: mm10
Supplementary_files_format_and_content: A tab-delimited xlsx spreadsheet which includes the raw unfiltered read counts for each gene in each sample, as calculated by STAR.

source_name: Bone marrow

growth_protocol: Mouse bone marrow was cultured in DMEM + 10% FBS with WEHI conditioned media, IL-3, IL6 and SCF supplementation during retroviral transduction

extract_protocol:
Total RNA was extracted using the RNeasy micro kit (Qiagen).
cDNA libraries were constructed using the SMARTer universal low input RNA kit (Clontech)

treatment_protocol: Lineage negative GFP/RFP positive cells were isolated by flow cytometry and frozen prior to RNA extraction.

tag: strain

value: Bone marrow

tag: genotype/variation

value: Simultaneously retrovirally transduced with both CEBPA_V314VW and CSF3R_T618I


title: Mouse-Lin-Neg-CEBPA_V314VW+CSF3R_T618I-A


title: Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, resilient 1684

description:
Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, resilient
Ribosomal-bound RNA
1684_Aldh1l1_TRAP_JD130_PFC_resilient_IP_Rep4


title: Mouse-Lin-Neg-CEBPA_V314VW-C

description: RNA-seq on marine bone marrow cells transduced with CEBPA_V314VW vector

value: Retrovirally transduced with CEBPA_V314VW


title: Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, resilient 1683

description:
Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, resilient
Ribosomal-bound RNA
1683_Aldh1l1_TRAP_JD130_PFC_resilient_IP_Rep3


title: Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, resilient 1682

description:
Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, resilient
Ribosomal-bound RNA
1682_Aldh1l1_TRAP_JD130_PFC_resilient_IP_Rep2


title: Mouse-Lin-Neg-CEBPA_V314VW+CSF3R_T618I-C


title: Mouse-Lin-Neg-CSF3R_T618I-C

description: RNA-seq on marine bone marrow cells transduced with CSF3R_T618I vector

value: Retrovirally transduced with CSF3R_T618I


title: Mouse-Lin-Neg-CSF3R_T618I-B


title: Mouse-Lin-Neg-CSF3R_T618I-A


title: Mouse-Lin-Neg-CEBPA_V314VW-B


title: Mouse-Lin-Neg-Empty-C

description: RNA-seq on marine bone marrow cells transduced with empty vector

value: Retrovirally transduced with empty vector


title: Mouse-Lin-Neg-CEBPA_V314VW-A


title: CSF3R-first-C

data_processing:
Raw reads were trimmed with Trimmmomatic and aligned to mm10 with STAR to generate gene count tables.
Gene count tables were analyzed using the Bioconductor Package DESeq2.
Raw p values were adjusted for multiple comparisons using the Benjamini-Hochberg method.
Genome_build: mm10
Supplementary_files_format_and_content: A tab-delimited txt spreadsheet which includes the raw read counts for each gene, as calculated by STAR.

growth_protocol: Mouse bone marrow was cultured in DMEM + 10% FBS with WEHI conditioned media, IL-3, IL6 and SCF supplementation during spinoculation

extract_protocol:
Total RNA was extracted using the RNeasy micro kit (Qiagen).
cDNA libraries were constructed using the SMARTer universal low input RNA kit (Clonetech)

treatment_protocol: Lineage negative GFP/RFP positive cells were isolated by flow cytometry and cultured in IMDM +20% FBS for 48 hours in the presence of 4-hydroxy tamoxifen

value: Retrovirally transduced with CSF3R-first and CEPBA-second


title: Mouse-Lin-Neg-Empty-B


title: CEBPA-first-C

value: Retrovirally transduced with CEBPA-first and CSF3R-second


title: Mouse-Lin-Neg-Empty-A


title: CSF3R-first-B


title: CSF3R-first-A


title: CSF3R-only-D

value: Retrovirally transduced with CSF3R-only


title: CEBPA-first-B


title: CEBPA-first-D


title: Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, resilient 1681

description:
Aldh1l1-EGFP/Rpl10a (JD130), prefrontal cortex, resilient
Ribosomal-bound RNA
1681_Aldh1l1_TRAP_JD130_PFC_resilient_IP_Rep1


title: CEBPA-first-A


title: CSF3R-only-B


title: CSF3R-only-C


title: CSF3R-only-A


title: netrin-1 unc5B MUT rep2 [RNA-seq]

city: Lyon

first: Fabrice

last: Lavial

address: 28 rue Laennec

country: France

institute: CRCL

description: CGR8 mESC transfected with an empty ppy-cagg-netrin-ires-puro vector expressing the netrin-1 transgene.

data_processing:
Software: All analyses were performed using FastQC version 0.11.5 and fastq_screen version 0.9.5, STAR version 2.5.2b, R version 3.3.2 (2016-10-31), x86_64-apple-darwin13.4.0, Base packages: base, datasets, graphics, grDevices, grid, methods, parallel, stats, stats4, utils,
Read quality: Quality of raw reads was assessed using the FastQC quality control tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Estimation of Contamination: Sample contamination was assessed using the fastq_screen quality control tool (http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen). Bowtie2 indexes for Mus musculus (mm10) and Homo sapiens (GRCh38) were downloaded from the bowtie website.
Mapping and Summarization: The “primary assembly” Mus musculus genome sequence (release GRCm38.p5) and transcriptome annotations (Ensembl release 87) were downloaded from the GENCODE website (files GRCm38.primary_assembly.genome.fa and gencode.vM12.primary_assembly.annotation.gtf, respectively). Raw read data (fastq files) were mapped to these sequences using STAR (with parameters --outFilterType BySJout, --outSAMtype BAM Unsorted, and --quantMode GeneCounts). This last parameter allows direct conversion of the mappings into gene counts.
Normalization: For the quality control representations, the effective library sizes were first computed using function estimateSizeFactors from package DESeq2. The raw count values were then transformed using a variance stabilizing transformation (function varianceStabilizingTransformation from package DESeq2 with parameter blind=TRUE).
Gene filtering: Genes that did not have more than one count per million counts in at least 2 samples were filtered out. Genes were also filtered if their Ensembl description was either empty, “predicted gene”, “predicted pseudogene” or a “RIKEN”.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: counts_raw.txt: Tab-delimited text file includes raw counts for each sample.
Supplementary_files_format_and_content: counts_normalized.txt : Tab-delimited text file includes normalized counts for the samples.
Supplementary_files_format_and_content: model_fc.txt: Tab-delimited text file includes FC, p-value and adjusted p-value.

source_name: mouse embryonic stem cells

growth_protocol: mESC are grown in serum/LIF conditions.

extract_protocol:
RNA extracted with Qiagen RNeasy columns.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: mESC are stably transfected with ppy-cagg-ires-puro vector empty or encoding a netrin-1 transgene.

value: embryonic stem cells

tag: transfection

value: ppy-cagg-netrin-ires-puro vector expressing netrin-1 transgene

tag: netrin-1 transgene variation

value: netrin-1 unc5B MUT


title: netrin-1 neo1 MUT rep2 [RNA-seq]

value: netrin-1 neo1 MUT


title: netrin-1 neo1 MUT rep1 [RNA-seq]


title: netrin-1 unc5B MUT rep1 [RNA-seq]


title: netrin-1 unc5b MUT rep3 [RNA-seq]


title: netrin-1 rep2 [RNA-seq]

value: netrin WT


title: netrin-1 rep3 [RNA-seq]


title: netrin-1 rep1 [RNA-seq]


title: control rep2 [RNA-seq]

description: CGR8 mESC transfected with an empty ppy-cagg-ires-puro vector.

value: empty ppy-cagg-ires-puro vector


title: control rep3 [RNA-seq]


title: LSK cell 94 (Lsk.6wks.94)

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description:
Lin- CD117+ Sca1+
Lsk.94
LSK cell 94
Lsk.6wks.94

data_processing:
RNA reads were aligned to the reference mm9 mouse genome using Bowtie2.
Single-cell and matched bulk sorted RNA-Seq were analyzed using RSEM to estimate transcripts per million mapped reads (TPM) for all genes.
Differentially expressed genes were identified using AltAnalyze using a FDR adjusted empirical Bayes moderated t-test p<0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file of log2 (incremented by 1 before log2) TPM RSEM expression values

source_name: Bone Marrow

extract_protocol:
Cells were harvested from bone marrow. Femurs, tibias and iliac crest were harvested immediately after euthanasia and put in cold PBS+2%FBS. Bones were crushed with mortar and pestle, filtered and washed in cold PBS+2%FBS, then enriched using CD117 MicroBeads on a Automacs Pro separator (Miltenyi, San Diego, CA). CD117+ cells were stained with CD16/32-PerCp-ef710 (clone 93), CD3-biotin (clone 145-2C11), CD4-biotin (clone RM4-5), CD8-biotin (clone 53-6.7), CD11b-biotin (clone M1/70), CD19-biotin (clone 6D5), Gr1-biotin (clone RB6-8C5), Ter119-biotin (clone Ter-119) CD45R-biotin (clone RA3-6B2), CD117-APC (clone 2B8), Sca-1-Pe-Cy7 (clone D7), CD34-BV421 (clone RAM34), CD115-BV605 (clone TR15-12F1 2.2), CD135-PE (A2F10.1), CCR3-FITC (clone 83101), SiglecF (clone E50-2440) and Gr1-FITC (clone RB6-8C5). Cell sorting was performed on MoFloXDP (Beckman Coulter, Brea, CA) or BD FACSAria II with a 100μm nozzleand subjected to flow cytrometric sorting of bone marrow lineage-negative Sca1+ CD117+ cells (LSK).
cDNA was made with Clontech SMARTer® Kit “the mRNA Seq: RT + Amp (1771x), Libraries were constructed using Nextera XT DNA Library Preparation Kit
Single cells were separated using Fluidigm C1 system

value: LSK Stem cells

tag: age

value: 6 wks


title: LSK cell 95 (Lsk.6wks.95)

description:
Lin- CD117+ Sca1+
Lsk.95
LSK cell 95
Lsk.6wks.95


title: control rep1 [RNA-seq]


title: LSK cell 92 (Lsk.6wks.92)

description:
Lin- CD117+ Sca1+
Lsk.92
LSK cell 92
Lsk.6wks.92


title: LSK cell 93 (Lsk.6wks.93)

description:
Lin- CD117+ Sca1+
Lsk.93
LSK cell 93
Lsk.6wks.93


title: LSK cell 88 (Lsk.6wks.88)

description:
Lin- CD117+ Sca1+
Lsk.88
LSK cell 88
Lsk.6wks.88


title: LSK cell 90 (Lsk.6wks.90)

description:
Lin- CD117+ Sca1+
Lsk.90
LSK cell 90
Lsk.6wks.90


title: LSK cell 89 (Lsk.6wks.89)

description:
Lin- CD117+ Sca1+
Lsk.89
LSK cell 89
Lsk.6wks.89


title: LSK cell 86 (Lsk.6wks.86)

description:
Lin- CD117+ Sca1+
Lsk.86
LSK cell 86
Lsk.6wks.86


title: LSK cell 87 (Lsk.6wks.87)

description:
Lin- CD117+ Sca1+
Lsk.87
LSK cell 87
Lsk.6wks.87


title: LSK cell 84 (Lsk.6wks.84)

description:
Lin- CD117+ Sca1+
Lsk.84
LSK cell 84
Lsk.6wks.84


title: LSK cell 83 (Lsk.6wks.83)

description:
Lin- CD117+ Sca1+
Lsk.83
LSK cell 83
Lsk.6wks.83


title: LSK cell 81 (Lsk.6wks.81)

description:
Lin- CD117+ Sca1+
Lsk.81
LSK cell 81
Lsk.6wks.81


title: LSK cell 80 (Lsk.6wks.80)

description:
Lin- CD117+ Sca1+
Lsk.80
LSK cell 80
Lsk.6wks.80


title: LSK cell 85 (Lsk.6wks.85)

description:
Lin- CD117+ Sca1+
Lsk.85
LSK cell 85
Lsk.6wks.85


title: netrin-1 neo1 MUT rep3 [RNA-seq]


title: LSK cell 82 (Lsk.6wks.82)

description:
Lin- CD117+ Sca1+
Lsk.82
LSK cell 82
Lsk.6wks.82


title: LSK cell 79 (Lsk.6wks.79)

description:
Lin- CD117+ Sca1+
Lsk.79
LSK cell 79
Lsk.6wks.79


title: LSK cell 77 (Lsk.6wks.77)

description:
Lin- CD117+ Sca1+
Lsk.77
LSK cell 77
Lsk.6wks.77


title: LSK cell 76 (Lsk.6wks.76)

description:
Lin- CD117+ Sca1+
Lsk.76
LSK cell 76
Lsk.6wks.76


title: LSK cell 96 (Lsk.6wks.96)

description:
Lin- CD117+ Sca1+
Lsk.96
LSK cell 96
Lsk.6wks.96


title: LSK cell 78 (Lsk.6wks.78)

description:
Lin- CD117+ Sca1+
Lsk.78
LSK cell 78
Lsk.6wks.78


title: LSK cell 74 (Lsk.6wks.74)

description:
Lin- CD117+ Sca1+
Lsk.74
LSK cell 74
Lsk.6wks.74


title: LSK cell 73 (Lsk.6wks.73)

description:
Lin- CD117+ Sca1+
Lsk.73
LSK cell 73
Lsk.6wks.73


title: LSK cell 75 (Lsk.6wks.75)

description:
Lin- CD117+ Sca1+
Lsk.75
LSK cell 75
Lsk.6wks.75


title: LSK cell 71 (Lsk.6wks.71)

description:
Lin- CD117+ Sca1+
Lsk.71
LSK cell 71
Lsk.6wks.71


title: LSK cell 72 (Lsk.6wks.72)

description:
Lin- CD117+ Sca1+
Lsk.72
LSK cell 72
Lsk.6wks.72


title: LSK cell 91 (Lsk.6wks.91)

description:
Lin- CD117+ Sca1+
Lsk.91
LSK cell 91
Lsk.6wks.91


title: LSK cell 67 (Lsk.6wks.67)

description:
Lin- CD117+ Sca1+
Lsk.67
LSK cell 67
Lsk.6wks.67


title: LSK cell 64 (Lsk.6wks.64)

description:
Lin- CD117+ Sca1+
Lsk.64
LSK cell 64
Lsk.6wks.64


title: LSK cell 70 (Lsk.6wks.70)

description:
Lin- CD117+ Sca1+
Lsk.70
LSK cell 70
Lsk.6wks.70


title: LSK cell 66 (Lsk.6wks.66)

description:
Lin- CD117+ Sca1+
Lsk.66
LSK cell 66
Lsk.6wks.66


title: LSK cell 69 (Lsk.6wks.69)

description:
Lin- CD117+ Sca1+
Lsk.69
LSK cell 69
Lsk.6wks.69


title: LSK cell 65 (Lsk.6wks.65)

description:
Lin- CD117+ Sca1+
Lsk.65
LSK cell 65
Lsk.6wks.65


title: LSK cell 63 (Lsk.6wks.63)

description:
Lin- CD117+ Sca1+
Lsk.63
LSK cell 63
Lsk.6wks.63


title: LSK cell 60 (Lsk.6wks.60)

description:
Lin- CD117+ Sca1+
Lsk.60
LSK cell 60
Lsk.6wks.60


title: LSK cell 61 (Lsk.6wks.61)

description:
Lin- CD117+ Sca1+
Lsk.61
LSK cell 61
Lsk.6wks.61


title: LSK cell 62 (Lsk.6wks.62)

description:
Lin- CD117+ Sca1+
Lsk.62
LSK cell 62
Lsk.6wks.62


title: LSK cell 58 (Lsk.6wks.58)

description:
Lin- CD117+ Sca1+
Lsk.58
LSK cell 58
Lsk.6wks.58


title: LSK cell 59 (Lsk.6wks.59)

description:
Lin- CD117+ Sca1+
Lsk.59
LSK cell 59
Lsk.6wks.59


title: LSK cell 54 (Lsk.6wks.54)

description:
Lin- CD117+ Sca1+
Lsk.54
LSK cell 54
Lsk.6wks.54


title: LSK cell 55 (Lsk.6wks.55)

description:
Lin- CD117+ Sca1+
Lsk.55
LSK cell 55
Lsk.6wks.55


title: LSK cell 52 (Lsk.6wks.52)

description:
Lin- CD117+ Sca1+
Lsk.52
LSK cell 52
Lsk.6wks.52


title: LSK cell 53 (Lsk.6wks.53)

description:
Lin- CD117+ Sca1+
Lsk.53
LSK cell 53
Lsk.6wks.53


title: LSK cell 51 (Lsk.6wks.51)

description:
Lin- CD117+ Sca1+
Lsk.51
LSK cell 51
Lsk.6wks.51


title: LSK cell 50 (Lsk.6wks.50)

description:
Lin- CD117+ Sca1+
Lsk.50
LSK cell 50
Lsk.6wks.50


title: LSK cell 47 (Lsk.6wks.47)

description:
Lin- CD117+ Sca1+
Lsk.47
LSK cell 47
Lsk.6wks.47


title: LSK cell 44 (Lsk.6wks.44)

description:
Lin- CD117+ Sca1+
Lsk.44
LSK cell 44
Lsk.6wks.44


title: LSK cell 45 (Lsk.6wks.45)

description:
Lin- CD117+ Sca1+
Lsk.45
LSK cell 45
Lsk.6wks.45


title: LSK cell 42 (Lsk.6wks.42)

description:
Lin- CD117+ Sca1+
Lsk.42
LSK cell 42
Lsk.6wks.42


title: LSK cell 46 (Lsk.6wks.46)

description:
Lin- CD117+ Sca1+
Lsk.46
LSK cell 46
Lsk.6wks.46


title: LSK cell 43 (Lsk.6wks.43)

description:
Lin- CD117+ Sca1+
Lsk.43
LSK cell 43
Lsk.6wks.43


title: LSK cell 41 (Lsk.6wks.41)

description:
Lin- CD117+ Sca1+
Lsk.41
LSK cell 41
Lsk.6wks.41


title: LSK cell 39 (Lsk.6wks.39)

description:
Lin- CD117+ Sca1+
Lsk.39
LSK cell 39
Lsk.6wks.39


title: LSK cell 40 (Lsk.6wks.40)

description:
Lin- CD117+ Sca1+
Lsk.40
LSK cell 40
Lsk.6wks.40


title: LSK cell 37 (Lsk.6wks.37)

description:
Lin- CD117+ Sca1+
Lsk.37
LSK cell 37
Lsk.6wks.37


title: LSK cell 32 (Lsk.6wks.32)

description:
Lin- CD117+ Sca1+
Lsk.32
LSK cell 32
Lsk.6wks.32


title: LSK cell 36 (Lsk.6wks.36)

description:
Lin- CD117+ Sca1+
Lsk.36
LSK cell 36
Lsk.6wks.36


title: LSK cell 57 (Lsk.6wks.57)

description:
Lin- CD117+ Sca1+
Lsk.57
LSK cell 57
Lsk.6wks.57


title: LSK cell 35 (Lsk.6wks.35)

description:
Lin- CD117+ Sca1+
Lsk.35
LSK cell 35
Lsk.6wks.35


title: LSK cell 29 (Lsk.6wks.29)

description:
Lin- CD117+ Sca1+
Lsk.29
LSK cell 29
Lsk.6wks.29


title: LSK cell 33 (Lsk.6wks.33)

description:
Lin- CD117+ Sca1+
Lsk.33
LSK cell 33
Lsk.6wks.33


title: LSK cell 27 (Lsk.6wks.27)

description:
Lin- CD117+ Sca1+
Lsk.27
LSK cell 27
Lsk.6wks.27


title: LSK cell 31 (Lsk.6wks.31)

description:
Lin- CD117+ Sca1+
Lsk.31
LSK cell 31
Lsk.6wks.31


title: LSK cell 28 (Lsk.6wks.28)

description:
Lin- CD117+ Sca1+
Lsk.28
LSK cell 28
Lsk.6wks.28


title: LSK cell 26 (Lsk.6wks.26)

description:
Lin- CD117+ Sca1+
Lsk.26
LSK cell 26
Lsk.6wks.26


title: LSK cell 30 (Lsk.6wks.30)

description:
Lin- CD117+ Sca1+
Lsk.30
LSK cell 30
Lsk.6wks.30


title: LSK cell 24 (Lsk.6wks.24)

description:
Lin- CD117+ Sca1+
Lsk.24
LSK cell 24
Lsk.6wks.24


title: LSK cell 23 (Lsk.6wks.23)

description:
Lin- CD117+ Sca1+
Lsk.23
LSK cell 23
Lsk.6wks.23


title: LSK cell 49 (Lsk.6wks.49)

description:
Lin- CD117+ Sca1+
Lsk.49
LSK cell 49
Lsk.6wks.49


title: LSK cell 22 (Lsk.6wks.22)

description:
Lin- CD117+ Sca1+
Lsk.22
LSK cell 22
Lsk.6wks.22


title: LSK cell 21 (Lsk.6wks.21)

description:
Lin- CD117+ Sca1+
Lsk.21
LSK cell 21
Lsk.6wks.21


title: LSK cell 20 (Lsk.6wks.20)

description:
Lin- CD117+ Sca1+
Lsk.20
LSK cell 20
Lsk.6wks.20


title: LSK cell 48 (Lsk.6wks.48)

description:
Lin- CD117+ Sca1+
Lsk.48
LSK cell 48
Lsk.6wks.48


title: LSK cell 19 (Lsk.6wks.19)

description:
Lin- CD117+ Sca1+
Lsk.19
LSK cell 19
Lsk.6wks.19


title: LSK cell 14 (Lsk.6wks.14)

description:
Lin- CD117+ Sca1+
Lsk.14
LSK cell 14
Lsk.6wks.14


title: LSK cell 18 (Lsk.6wks.18)

description:
Lin- CD117+ Sca1+
Lsk.18
LSK cell 18
Lsk.6wks.18


title: LSK cell 16 (Lsk.6wks.16)

description:
Lin- CD117+ Sca1+
Lsk.16
LSK cell 16
Lsk.6wks.16


title: LSK cell 38 (Lsk.6wks.38)

description:
Lin- CD117+ Sca1+
Lsk.38
LSK cell 38
Lsk.6wks.38


title: LSK cell 15 (Lsk.6wks.15)

description:
Lin- CD117+ Sca1+
Lsk.15
LSK cell 15
Lsk.6wks.15


title: LSK cell 13 (Lsk.6wks.13)

description:
Lin- CD117+ Sca1+
Lsk.13
LSK cell 13
Lsk.6wks.13


title: LSK cell 34 (Lsk.6wks.34)

description:
Lin- CD117+ Sca1+
Lsk.34
LSK cell 34
Lsk.6wks.34


title: LSK cell 12 (Lsk.6wks.12)

description:
Lin- CD117+ Sca1+
Lsk.12
LSK cell 12
Lsk.6wks.12


title: LSK cell 9 (Lsk.6wks.9)

description:
Lin- CD117+ Sca1+
Lsk.9
LSK cell 9
Lsk.6wks.9


title: LSK cell 8 (Lsk.6wks.8)

description:
Lin- CD117+ Sca1+
Lsk.8
LSK cell 8
Lsk.6wks.8


title: LSK cell 7 (Lsk.6wks.7)

description:
Lin- CD117+ Sca1+
Lsk.7
LSK cell 7
Lsk.6wks.7


title: LSK cell 11 (Lsk.6wks.11)

description:
Lin- CD117+ Sca1+
Lsk.11
LSK cell 11
Lsk.6wks.11


title: LSK cell 6 (Lsk.6wks.6)

description:
Lin- CD117+ Sca1+
Lsk.6
LSK cell 6
Lsk.6wks.6


title: LSK cell 5 (Lsk.6wks.5)

description:
Lin- CD117+ Sca1+
Lsk.5
LSK cell 5
Lsk.6wks.5


title: LSK cell 4 (Lsk.6wks.4)

description:
Lin- CD117+ Sca1+
Lsk.4
LSK cell 4
Lsk.6wks.4


title: LSK cell 2 (Lsk.6wks.2)

description:
Lin- CD117+ Sca1+
Lsk.2
LSK cell 2
Lsk.6wks.2


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.9)

description:
HSC from 14-month old obese mouse (db/db)
Mouse-scRNASeq_WT_vs_Obese 14_Mo-RSEM-TPM

data_processing:
FASTQ sequence files were aligned to the mouse genome version mm9 using RSEM.
The fastq files were aligned to mouse genome mm9 using BowTie 2 and RSEM. To identify differentially expressed genes using default parameters moderated t-test with Benjamini-Hochberg multiple testing correction, raw p-value cut-off of 0.05, and an expression cut-off of 2-fold. RSEM gene-expression TPM values were all subjected to the same defaults in AltAnlayze for statistical analysis.
For all RNAseq experiments pathways and ontology enrichment analyses were performed with ToppGene (Chen et al., 2009) and GO-Elite (Zambon et al., 2012). All heatmaps from AltAnalyze were created using the HOPACH package via a connection to R (Salomonis et al., 2005). All gene set enrichment analyses were performed using GSEA v.2.2.0 (Mootha et al., 2003; Subramanian et al., 2005).
Genome_build: mm9
Supplementary_files_format_and_content: TPMs

source_name: HSC Obese (db/db) 14 months

growth_protocol: Mice were euthanized with carbon dioxide and cervical dislocation. BM cells were obtained by crushing long bones and hips, treated with Ammonium-Chloride-Potassium (ACK) buffer (150 mM NH4Cl/10 mM KHCO3) to lyse red blood cells and purified by ficoll separation (Histopaque-1119, Sigma-Aldrich). AutoMACS (Miltenyi) enriched c-kit+ cells were stained with unconjugated rat lineage specific antibodies (Lin: Ter-119, Mac1, Gr-1, B220, CD5, CD3, CD4, CD8, CD127), followed by staining with goat anti-rat-PE-Cy5 secondary antibody. Cells were then stained with c-Kit-APC-eFluor780, Sca1-PB, CD48-Alexa-Fluor647, CD150-PE antibodies and sorted at purity on a FACS ARIAII  (BD biosciences).

extract_protocol:
Single HSCs were prepared using the C1™ Single-Cell Auto Prep System (5-10 µm Fluidic Chip for mRNA-Seq; Fluidigm, San Fransisco, CA), according to the manufacturer’s instructions. Cell separation was visually inspected to identify wells containing single live cells. In two independent rounds,78 and 69 cells were captured for  WT and db/db samples, respectively.
Cell lysis and reverse transcription were performed in the ChiP using the Clontech SMARTer® Kit  according to the manufacturer’s instructions. cDNAs were then transferred to a 96 well plate and diluted with 6 µl C1™ DNA Dilution Reagent. cDNAs were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies, Grand Island, NY) and Agilent High Sensitivity DNA Kit (Agilent Technologies (Santa Clara, CA). Libraries for  48 visually validated cells in each conditions were prepared using the Nextera XT DNA Library Preparation Kit (Illumina Inc, Santa Clara, CA). Libraries were pooled, purified on the AMPure® bead-based magnetic separation Kit and controlled using  Agilent High Sensitivity DNA Kit. Single-cell RNA-Seq libraries were sequenced on one HiSeq 2500 gel.

tag: genotype

value: db/db (obese)

value: CD150+CD48-LSK HSC

value: 14 months


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.7)

value: Bone marrow


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.5)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.6)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.42)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.43)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.41)


title: LSK cell 17 (Lsk.6wks.17)

description:
Lin- CD117+ Sca1+
Lsk.17
LSK cell 17
Lsk.6wks.17


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.40)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.4)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.39)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.38)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.37)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.36)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.33)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.35)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.32)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.31)


title: LSK cell 1 (Lsk.6wks.1)

description:
Lin- CD117+ Sca1+
Lsk.1
LSK cell 1
Lsk.6wks.1


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.3)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.29)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.28)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.8)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.27)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.24)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.25)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.23)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.22)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.20)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.2)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.21)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.18)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.34)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.15)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.17)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.16)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.13)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.10)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.30)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.11)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.12)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.26)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.1)


title: HSC Control 14 months (Lsk.15mo.SLAM.95)

description:
HSC from 14-month old WT mouse
Mouse-scRNASeq_WT_vs_Obese 14_Mo-RSEM-TPM

source_name: HSC Control 14 months

value: WT


title: HSC Control 14 months (Lsk.15mo.SLAM.94)


title: HSC Control 14 months (Lsk.15mo.SLAM.93)


title: HSC Control 14 months (Lsk.15mo.SLAM.91)


title: HSC Control 14 months (Lsk.15mo.SLAM.90)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.19)


title: HSC Control 14 months (Lsk.15mo.SLAM.86)


title: HSC Control 14 months (Lsk.15mo.SLAM.85)


title: HSC Control 14 months (Lsk.15mo.SLAM.82)


title: HSC Obese (db/db) 14 months (Lsk.15mo.SLAM.OB.LepR.14)


title: HSC Control 14 months (Lsk.15mo.SLAM.81)


title: LSK cell 10 (Lsk.6wks.10)

description:
Lin- CD117+ Sca1+
Lsk.10
LSK cell 10
Lsk.6wks.10


title: HSC Control 14 months (Lsk.15mo.SLAM.89)


title: HSC Control 14 months (Lsk.15mo.SLAM.87)


title: HSC Control 14 months (Lsk.15mo.SLAM.79)


title: HSC Control 14 months (Lsk.15mo.SLAM.80)


title: HSC Control 14 months (Lsk.15mo.SLAM.77)


title: HSC Control 14 months (Lsk.15mo.SLAM.74)


title: HSC Control 14 months (Lsk.15mo.SLAM.76)


title: HSC Control 14 months (Lsk.15mo.SLAM.75)


title: HSC Control 14 months (Lsk.15mo.SLAM.96)


title: HSC Control 14 months (Lsk.15mo.SLAM.73)


title: HSC Control 14 months (Lsk.15mo.SLAM.72)


title: HSC Control 14 months (Lsk.15mo.SLAM.71)


title: HSC Control 14 months (Lsk.15mo.SLAM.92)


title: HSC Control 14 months (Lsk.15mo.SLAM.88)


title: HSC Control 14 months (Lsk.15mo.SLAM.69)


title: HSC Control 14 months (Lsk.15mo.SLAM.70)


title: HSC Control 14 months (Lsk.15mo.SLAM.68)


title: HSC Control 14 months (Lsk.15mo.SLAM.67)


title: HSC Control 14 months (Lsk.15mo.SLAM.66)


title: HSC Control 14 months (Lsk.15mo.SLAM.65)


title: HSC Control 14 months (Lsk.15mo.SLAM.62)


title: HSC Control 14 months (Lsk.15mo.SLAM.84)


title: HSC Control 14 months (Lsk.15mo.SLAM.78)


title: HSC Control 14 months (Lsk.15mo.SLAM.63)


title: HSC Control 14 months (Lsk.15mo.SLAM.83)


title: HSC Control 14 months (Lsk.15mo.SLAM.64)


title: HSC Control 14 months (Lsk.15mo.SLAM.60)


title: HSC Control 14 months (Lsk.15mo.SLAM.61)


title: HSC Control 14 months (Lsk.15mo.SLAM.57)


title: HSC Control 14 months (Lsk.15mo.SLAM.59)


title: HSC Control 14 months (Lsk.15mo.SLAM.58)


title: HSC Control 14 months (Lsk.15mo.SLAM.55)


title: HSC Control 14 months (Lsk.15mo.SLAM.56)


title: HSC Control 14 months (Lsk.15mo.SLAM.54)


title: HSC Control 14 months (Lsk.15mo.SLAM.53)


title: HSC Control 14 months (Lsk.15mo.SLAM.51)


title: HSC Control 14 months (Lsk.15mo.SLAM.52)


title: HSC Control 14 months (Lsk.15mo.SLAM.50)


title: HSC Control 14 months (Lsk.15mo.SLAM.47)


title: HSC Control 14 months (Lsk.15mo.SLAM.49)


title: HSC Control 14 months (Lsk.15mo.SLAM.46)


title: HSC Control 14 months (Lsk.15mo.SLAM.48)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.47)

description:
HSC from 4-month old obese mouse (db/db)
Mouse-scRNASeq_WT_vs_Obese 4_Mo-RSEM-TPM

source_name: HSC Obese (db/db) 4 months

value: 4 months


title: HSC Control 14 months (Lsk.15mo.SLAM.45)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.48)


title: HSC Control 14 months (Lsk.15mo.SLAM.44)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.43)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.46)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.44)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.42)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.39)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.37)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.38)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.35)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.40)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.41)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.34)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.32)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.33)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.36)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.31)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.27)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.29)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.28)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.30)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.26)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.23)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.25)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.22)


title: LSK cell 3 (Lsk.6wks.3)

description:
Lin- CD117+ Sca1+
Lsk.3
LSK cell 3
Lsk.6wks.3


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.45)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.24)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.18)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.20)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.19)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.21)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.16)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.17)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.15)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.14)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.11)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.12)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.9)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.13)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.10)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.8)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.4)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.3)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.2)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.1)


title: HSC Control 4 months (Lsk.16wks.SLAM.96)

description:
HSC from 4-month old WT mouse
Mouse-scRNASeq_WT_vs_Obese 4_Mo-RSEM-TPM

source_name: HSC Control 4 months


title: HSC Control 4 months (Lsk.16wks.SLAM.94)


title: HSC Control 4 months (Lsk.16wks.SLAM.93)


title: HSC Control 4 months (Lsk.16wks.SLAM.92)


title: HSC Control 4 months (Lsk.16wks.SLAM.91)


title: HSC Control 4 months (Lsk.16wks.SLAM.90)


title: HSC Control 4 months (Lsk.16wks.SLAM.88)


title: HSC Control 4 months (Lsk.16wks.SLAM.89)


title: HSC Control 4 months (Lsk.16wks.SLAM.87)


title: HSC Control 4 months (Lsk.16wks.SLAM.85)


title: HSC Control 4 months (Lsk.16wks.SLAM.86)


title: HSC Control 4 months (Lsk.16wks.SLAM.83)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.5)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.6)


title: HSC Obese (db/db) 4 months (Lsk.16wks.SLAM.OB.LepR.7)


title: HSC Control 4 months (Lsk.16wks.SLAM.81)


title: HSC Control 4 months (Lsk.16wks.SLAM.80)


title: HSC Control 4 months (Lsk.16wks.SLAM.79)


title: HSC Control 4 months (Lsk.16wks.SLAM.76)


title: HSC Control 4 months (Lsk.16wks.SLAM.78)


title: HSC Control 4 months (Lsk.16wks.SLAM.82)


title: HSC Control 4 months (Lsk.16wks.SLAM.74)


title: HSC Control 4 months (Lsk.16wks.SLAM.73)


title: HSC Control 4 months (Lsk.16wks.SLAM.77)


title: HSC Control 4 months (Lsk.16wks.SLAM.75)


title: HSC Control 4 months (Lsk.16wks.SLAM.95)


title: HSC Control 4 months (Lsk.16wks.SLAM.72)


title: HSC Control 4 months (Lsk.16wks.SLAM.71)


title: HSC Control 4 months (Lsk.16wks.SLAM.67)


title: HSC Control 4 months (Lsk.16wks.SLAM.70)


title: HSC Control 4 months (Lsk.16wks.SLAM.65)


title: HSC Control 4 months (Lsk.16wks.SLAM.68)


title: HSC Control 4 months (Lsk.16wks.SLAM.69)


title: HSC Control 4 months (Lsk.16wks.SLAM.64)


title: HSC Control 4 months (Lsk.16wks.SLAM.62)


title: HSC Control 4 months (Lsk.16wks.SLAM.60)


title: HSC Control 4 months (Lsk.16wks.SLAM.61)


title: HSC Control 4 months (Lsk.16wks.SLAM.63)


title: HSC Control 4 months (Lsk.16wks.SLAM.59)


title: HSC Control 4 months (Lsk.16wks.SLAM.58)


title: HSC Control 4 months (Lsk.16wks.SLAM.57)


title: HSC Control 4 months (Lsk.16wks.SLAM.56)


title: HSC Control 4 months (Lsk.16wks.SLAM.55)


title: HSC Control 4 months (Lsk.16wks.SLAM.52)


title: HSC Control 4 months (Lsk.16wks.SLAM.53)


title: HSC Control 4 months (Lsk.16wks.SLAM.50)


title: HSC Control 4 months (Lsk.16wks.SLAM.51)


title: 10-day-control

city: WInnipeg

first: Sarah

last: Medina

state: Manitoba

address: 1015 Arlington Street

department: One Health

country: Canada

institute: Public Health Agency of Canada

description:
miRNA reads per million list.xlsx
10-day-contol_S6_L001_R1_001.fastq

data_processing:
Resulting FASTQ files were uploaded into Genboree Workbench (genboree.org) where miRNA read counts were determined using the ExceRpt small RNA-seq pipeline v4.6.2
Genome_build: mm10
Supplementary_files_format_and_content: excel matrix table of miRNA reads per million of all samples generated from Genboree Workbench ExceRpt small RNA-seq pipeline v4.6.2

source_name: Ringer-HEPES

growth_protocol: 4T1 breast cancer cells, purchased from ATCC (Middlesex, UK), were maintained in RPMI 1640 medium (PAN Biotech, Aidenbach, Germany) supplemented with ultraglutamine I (Lonza, Basel, Switzerland) and 5% heat-inactivated fetal bovine serum (PAN Biotech) in a 5% CO2 atmosphere at 37 ºC.

extract_protocol:
500ul of blood was collected from live mice under isofluorene anesthetic, collected with 40ul of the anticoagulant and spun down for 10mins @ 2000 RPM at 4°C to collect the plasma
Libraries were prepared as per manufacturer using Illumina's TruSeq smallRNA kit with 15 cycles of PCR amplification performed.  Desired product size of libraries (~146bp) were isolated using Sage Science's Blue Pippin machine on a 3% agarose gel and confirmed on Agilent's Bioanalyzer using a High Sensitivity DNA chip, followed by sequencing on Illumina's MiSeq using the MiSeq v3 reagent kit

treatment_protocol: 4T1 cells (1 x 106 cells in a total volume of 200 µL of Ringer-HEPES) were xenografted, under isoflurane anesthesia, in the right common carotid artery of female 7-8 weeks old Balb/c mice, purchased from Charles River Laboratories (Wilmington, MA, USA). Control mice were inoculated with Ringer-HEPES.

value: balb/c

tag: injected cell type

value: blood plasma

tag: dpi


title: HSC Control 4 months (Lsk.16wks.SLAM.49)


title: 10-day-4T1

description:
miRNA reads per million list.xlsx
10-day-4T1_S5_L001_R1_001.fastq

source_name: murine mammary carcinoma triple negative 4T1 cells


title: 7-day-control

description:
miRNA reads per million list.xlsx
7-day-contol_S4_L001_R1_001.fastq


title: 3-day-control

description:
miRNA reads per million list.xlsx
3-day-contol_S2_L001_R1_001.fastq


title: 3-day-4T1

description:
miRNA reads per million list.xlsx
3-day-4T1_S1_L001_R1_001.fastq

value: murine mammary carcinoma triple negative 4T1 cells


title: HSC Control 4 months (Lsk.16wks.SLAM.66)


title: BALB/c rep3

city: Oklahoma City

first: Lerin

last: Luckett-Chastain

state: OK

address: 1110 N. Stonewall

department: Pharmaceutical Science

institute: OUHSC

description: No Treatment

data_processing:
Qiagen's CLC Genomic Workbench version 10.0.1 was used for alignment and analysis.
CLC's standard RNA-Seq Analysis pipeline was used to align with the Mus musculus (GRCm38) genome. Differential expression analyses were performed using CLC's RNA-Seq Analysis workflow.
Differential expression settings were as follows: 3 samples per group. Data were normalized to reads per million (RPKM), and statistical analysis run with minimum fold change of 5 and FDR pvalue cutoff of 0.1
Genome_build: Mus musculus build 37.2
Supplementary_files_format_and_content: TPM   RPKM

source_name: Skin

growth_protocol: Mice were obtained from Jackson Laboratory at 4-5 weeks old. Mice were allowed to acclimate for 2 weeks and treatments began at 6 weeks old.

extract_protocol:
Skin was isolated after 7 consecutive days and RNA was isolated using Tri-Reagent.
RNAseq libraries were prepared using total RNA and standard Illumina protocols for TruSeq library construction kit.

treatment_protocol: 3 C57, 3 Balb/c, and 6 IL-6KO mice were shaved on Day 0. All mouse strains were left untreated for 7 Days.  On Day 8 all mice were euthanized and skin was isolated.

value: BALB/c

value: Skin

value: wild type


title: IL-6 -/- KO rep3

description: No Treatment


title: BALB/c rep1

description: No Treatment


title: IL-6 -/- KO rep2

description: No Treatment


title: C57BL/6 rep3

description: No Treatment


title: BALB/c rep2

description: No Treatment


title: IL-6 -/- KO rep1

description: No Treatment


title: HC12_96hrs_R179

city: Bellville

first: Abhilasha

last: Madhvi

state: Western Cape

address: Francie van Zijl Drive. Tygerberg

country: South Africa

institute: Stellenbosch University

description: total RNA targeted and seqeunced using Ion AmpliSeq™ Transcriptome Human Gene Expression Kit

data_processing:
Basecalling by Torrent Suite V5.4
Read mapping by tmap V5.4 to aligned to hg19 AmpliSeq Transcriptome 21 K
reads shorter than 8 filtered out, Quality trimmed to QV>16 with 30bp moving window.
Quantified to transcriptome in Partek (EM method)
Differential expression, (Gene Specific Analysis- Partek), read count of 0 reset to 1.0E-4
Genome_build: hg19 AmpliSeq Transcriptome 21 K

source_name: Peripheral Blood Mononuclear Cells

growth_protocol: Phlebotomy was performed on the healthy individuals (80 ml blood) in Na-Heparin vacutainers after obtaining written informed consent. The whole blood was further mixed with PBS in 1:1 ratio. This diluted mixture was gently poured over the Histopaque layer and subjected to centrifugation at 1440 g for 20 min. The buffy coat layer that appears between the blood plasma and the RBCs, containing PBMCs was collected in different tubes and washed twice with PBS. Total cells obtained were counted using a cell Countess (Invitrogen, Company, Country) and validated through manual counting. Human macrophage-like cells were cultured from human blood in Teflon jars using RPMI-1640 medium supplemented with 20% heparinized plasma and incubated at 370C, 5% CO2 for 5 days. This allows the differentiation of monocytes into macrophages

extract_protocol:
Total RNA from human macrophages was extracted with the help of a kit (RNeasy Plus Mini Kit) as per the manufacturer’s instructions. The extraction was performed immediately following the 12- and 96-hours infection period. The ‘gDNA eliminator’ column included in the kit was used to remove genomic DNA in all samples. For each experiment, RNA quantity and quality was measured using Agilent 2100 Bioanalyzer. The RNA with a high RNA integrity Number (RIN) (≥ 9) was used for Ampliseq and quantitative real time qPCR experiments. Total RNA was extracted and frozen immediately at -800C until Ampliseq is performed
Total RNA (100ng) was reverced transcribed using the SuperScript® VILO™ cDNA Kit to generate cDNA. The target regions were amplified for 10 reaction cycles using the Human Gene Expression Core Panel. After partial digestion, barcode adaptors (from the IonCde Adapters Kit) were ligated and the libraries were purified with Agencourt ™ AMPure™ XP reagent and eluted in low TE buffer

treatment_protocol: Mycobacteria was cultured in 7H9 (added 10% OADC and 0.5% glycerol) without Tween. Human macrophages were infected with each mycobacterial strain at MOI=1 and permitted for four hours of uptake. The cells were washed three times with phosphate buffered saline (PBS). Cells were then incubated for another 8 (12 hours post infection) or 92 hours (96 hours post infection) in 5% CO2 incubator at 37C.

value: Peripheral Blood Mononuclear Cells

tag: infection

value: Infected with R179

tag: time point

value: 96 hours post infection


title: C57BL/6 rep1

description: No Treatment

tag: tissue


title: C57BL/6 rep2

description: No Treatment


title: HC12_96hrs_BCG

value: Infected with BCG


title: HC12_96hrs_UI

value: Uninfected


title: HC12_12hrs_R179

value: 12 hours post infection


title: HC12_12hrs_BCG


title: 7-day-4T1

description:
miRNA reads per million list.xlsx
7-day-4T1_S3_L001_R1_001.fastq


title: HC11_96hrs_R179


title: HC12_12hrs_Msmeg

value: Infected with M Smeg


title: HC11_96hrs_BCG


title: HC11_12hrs_R179


title: HC11_96hrs_UI


title: HC11_12hrs_BCG


title: HC11_12hrs_Msmeg


title: HC12_12hrs_UI


title: HSC Control 4 months (Lsk.16wks.SLAM.54)

value: CD150+CD48-LSK HSC


title: HC10_96hrs_BCG


title: HC10_12hrs_R179


title: HC11_12hrs_UI


title: HC10_12hrs_Msmeg


title: HC10_96hrs_UI


title: HC9_96hrs_BCG


title: HC10_12hrs_UI


title: HC9_12hrs_R179


title: HC9_96hrs_R179


title: HC8_96hrs_R179


title: HC9_12hrs_BCG


title: HC9_96hrs_UI


title: HC9_12hrs_UI


title: HC9_12hrs_Msmeg


title: HC8_12hrs_Msmeg


title: HC8_12hrs_BCG


title: HC8_96hrs_BCG


title: HC8_12hrs_R179


title: HC8_96hrs_UI


title: HC10_96hrs_R179


title: HC7_96hrs_UI


title: HC7_12hrs_BCG


title: HC8_12hrs_UI


title: HC7_12hrs_R179


title: HC10_12hrs_BCG


title: HC7_12hrs_Msmeg


title: HSC Control 4 months (Lsk.16wks.SLAM.84)

value: Bone marrow


title: HC7_96hrs_R179


title: HC7_96hrs_BCG


title: HC7_12hrs_UI


title: HC6_96hrs_R179


title: HC6_12hrs_BCG


title: HC6_12hrs_R179


title: HC6_96hrs_UI


title: HC6_12hrs_UI


title: HC5_96hrs_R179


title: HC5_96hrs_BCG


title: HC5_96hrs_UI


title: HC5_12hrs_BCG


title: HC5_12hrs_UI


title: HC5_12hrs_Msmeg


title: HC4_96hrs_UI


title: HC4_12hrs_R179


title: HC4_12hrs_BCG


title: HC4_96hrs_BCG


title: HC3_96hrs_BCG


title: HC4_12hrs_Msmeg


title: HC3_96hrs_R179


title: HC4_12hrs_UI


title: HC3_96hrs_UI


title: HC6_96hrs_BCG


title: HC3_12hrs_BCG


title: HC3_12hrs_R179


title: HC6_12hrs_Msmeg


title: HC3_12hrs_Msmeg


title: HC3_12hrs_UI


title: HC2_96hrs_R179


title: HC5_12hrs_R179


title: HC2_96hrs_UI


title: HC2_96hrs_BCG


title: HC2_12hrs_Msmeg


title: HC2_12hrs_BCG


title: HC1_12hrs_R179


title: HC1_96hrs_BCG


title: HC4_96hrs_R179


title: HC1_96hrs_R179


title: HC1_12hrs_BCG


title: HC1_12hrs_Msmeg


title: HC1_12hrs_UI


title: huh7_A5

city: Bronx

first: Sanjeev

last: Gupta

address: 1300 Morris Park Ave.

department: Medicine

institute: Albert Einstein College of Medicine

data_processing:
Basecalls performed using Ion Torrent Suite version 4.2.1 with following configuration; BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1
Raw RNA-seq reads were trimmed using fastq_quality_trimmer version 0.0.14 with default parameters
Trimmed RNA-seq reads were aligned to the GRCh37 genome assembly using Tophat version 2.0.13 with default parameters
Aligned RNA-seq reads were counted using htseq-count version 0.6.1 with default parameters
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files were generated using htseq-count; Scores represent number of aligned sequence fragments per gene

source_name: HuH-7 cultured cells, arsenic 5 µM

extract_protocol:
Total RNA was isolated with mirVana kit followed by ribosomal RNA removal with RiboMinus kit (both Ambion),
RNA libraries were prepared with Ion Total RNA-Seq Kit v2 (Life Technologies) according to the kit manual

value: human hepatocellular carcinoma


title: huh7_A_C

source_name: HuH-7 cultured cells, arsenic 5 µM + copper 5 µM


title: huh7_A15

source_name: HuH-7 cultured cells, arsenic 15 µM


title: huh7_AP

source_name: HuH-7 cultured cells, acetaminophen 10 mM


title: huh7_Cof_Ap

source_name: HuH-7 cultured cells, acetaminophen 10 mM + caffeine 2 mM


title: huh7_Norm_Exo

source_name: HuH-7 cultured cells, exosomes from 1 ml of serum/105  cells


title: huh7_Norm

source_name: HuH-7 cultured cells, untreated control


title: E468_KD.1

city: Nijmegen

first: Nader

last: Atlasy

state: Gerderland

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

data_processing:
Raw reads mapped to human genome using GSNAP
Mapped reads were counted using HTSeq-count
raw counts was normalized using DESeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include DESeq normalized values for each Sample ...
All.normalised.raw.data.txt.gz: normalized raw data of all samples and replicas
U251_NT_KD.Downregulated.genes.xls.gz: Downregulated genes names and the corresponding GO terms
U251_NT_KD.Upregulated.genes.xls.gz: Upregulated genes and corresponding GO terms
E98_NT_KD.Downregulated.genes.xls.gz: Downregulated genes names and the corresponding GO terms
E98_NT_KD.Upregulated.genes.xls.gz: Upregulated genes and corresponding GO terms
E468_NT_KD.Downregulated.genes.xls.gz: Downregulated genes names and the corresponding GO terms
E468_NT_KD.Upregulated.genes.xls.gz: Upregulated genes and corresponding GO terms

source_name: GLIOMA CELL LINE

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Micro column based kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Transient downregulation of adherens junction proteins and adhesion receptors was obtained for monolayer cultures on rBM using specific or matched non-targeting smart-pool RNAi (Dharmacon) or 5 individual RNA probes (Sigma). For stable downregulation of p120-catenin with lentiviral particles pLKO.1 (MISSION shRNA, Sigma)

value: Brain

value: E468 glioma cell line

tag: targeted with


title: HC2_12hrs_R179


title: huh7_Cof

source_name: HuH-7 cultured cells, caffeine 2 mM

tag: cell type


title: E468_KD


title: HC2_12hrs_UI


title: E468_NT.1

value: NT-shRNA


title: E468_NT


title: E98_KD

value: E98 glioma cell line


title: E98_NT.1


title: U251_KD.1

value: U251 glioma cell line


title: E98_NT


title: HC1_96hrs_UI


title: E98_KD.1


title: U251_KD


title: U251_NT


title: U251_NT.1


title: H1_NPC_JMJD3

city: Guangzhou

first: Tian

last: Zhang

state: Guangdong

address: 190 Kaiyuan Avenue,Science Park

institute: GIBH

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were base-called and de-multiplexed using standard Illumina softwares. Bowtie2 was used to align the reads to the human genome hg38. Reads mapped to identical positions with same orientation in the genome were collapsed into one read.
The regions of UTX enrichment (peaks) were called using the SICER software package, with the input genomic DNA as a background control (parameters: W = 200; G = 600; FDR 0.01 cutoff applied).
Binding profiles and heatmaps were generated using ngsplot  and deeptools.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: narrowPeak

molecule: genomic DNA

extract_protocol:
For  ChIP-seq, 1×107 cells of each sample were crosslinked in 1% formaldehyde with rotation for 10 minutes at room temperature. And then these crosslinked reactions were stopped by 0.125 M glycine with rotation for 5 minutes at room temperature. and cell sample were sonicated, and then ChIPed with FLAG M2-beads.
DNA libraries were prepared for sequencing using standard Illumina protocols.

tag: antibody

value: anti-FLAG

value: human neural progenitor cells

value: WT


title: H1_NPC_INPUT-JMJD3

value: input


title: huh7_AP_Exo

source_name: HuH-7 cultured cells, acetaminophen 10 mM + exosomes from 1 ml of serum/105  cells


title: PC1_R3

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

country: United Kingdom

institute: Cerevance ltd

data_processing:
STAR alignment
htseq-count -s no -a 20 -m intersection-nonempty
Genome_build: hg38/Homo_sapiens.GRCh38.87.gtf
Supplementary_files_format_and_content: tab delimited file with raw count

source_name: PC1 (primed)

growth_protocol: HNES1 and naïve iPSCs are cultured in PXGL medium. Primed  iPSC (PC1 and PC2 are cultured in E8 medium)

extract_protocol:
Cell lysate and RNA  are prepared using Trizol/Chloroform
Sequencing libraries are prepared using TruSeq RNA Sample Prep Kit( Illumina), following ribosomal RNA depletion using Ribozero(Illumina)

value: primed iPSCs


title: PC1_R1


title: PC2_R1

source_name: PC2 (primed)


title: PC2_R3


title: PC1_R2


title: niPS_C4_Lam_R3

source_name: niPS C4 (Laminin)

value: naive iPSCs


title: HNES1_Gel_R1

source_name: HNES1 (Geltrex)

value: embryo derived HNES1 cells


title: HNES1_Lam_R1

source_name: HNES1 (Laminin)


title: HNES1_Gel_R2


title: HNES1_Lam_R2


title: niPS_C4_Gel_R3

source_name: niPS C4 (Geltrex)


title: niPS_C4_Lam_R1


title: niPS_C4_Lam_R2


title: niPS_C4_Gel_R2


title: niPS_C4_Gel_R1


title: LNCAP_AI_8.3

city: Buffalo

first: Qiang

last: Hu

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (GRCh38.p7) by STAR (version 2.7.0).
The number of fragments in each known gene from GENCODE (version 25) was quantified using STAR QuantMode (GeneCounts) function.
The differential gene expression was analyzed by R/Bioconductor package DESeq2 (version 1.24.0).
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R. Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are raw counts for all the samples.

source_name: Prostate Cancer Cell Line

growth_protocol: DU145 and LNCaP-AI cells were cultured in phenol red-free RPMI1640 medium containing 10% charcoal-stripped FBS .

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using Trizol reagent (Invitrogen).
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

value: LNCAP-AI

value: Androgen Insensitive Pca

tag: shRNA

value: shCTL


title: niPS_C2_Lam_R3

source_name: niPS C2 (Laminin)


title: LNCAP_AI_8plus.1


title: LNCAP_AI_8plus.3


title: PC2_R2


title: LNCAP_AI_8plus.2


title: LNCAP_AI_8.2


title: LNCAP_AI_8.1


title: niPS_C2_Lam_R2


title: HNES1_Lam_R3


title: niPS_C2_Lam_R1


title: DU145_8plus.2


title: HNES1_Gel_R3


title: niPS_C2_Gel_R3

source_name: niPS C2 (Geltrex)


title: niPS_C2_Gel_R2


title: DU145_8.3


title: DU145_8.2


title: H1_NPC_INPUT

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were base-called and de-multiplexed using standard Illumina softwares. Bowtie2 was used to align the reads to the human genome hg38. Reads mapped to identical positions with same orientation in the genome were collapsed into one read.
The regions of UTX enrichment (peaks) were called using the SICER software package, with the input genomic DNA as a background control (parameters: W = 200; G = 600; FDR 0.01 cutoff applied).
Binding profiles and heatmaps were generated using ngsplot  and deeptools.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: bed

source_name: human neural progenitor cells

extract_protocol:
For  ChIP-seq, 1×10^7 cells of each sample were crosslinked in 1% formaldehyde with rotation for 10 minutes at room temperature. And then these crosslinked reactions were stopped by 0.125 M glycine with rotation for 5 minutes at room temperature. and cell sample were sonicated, and then ChIPed with FLAG M2-beads.
DNA libraries were prepared for sequencing using standard Illumina protocols.

tag: chip antibody

value: none (input)


title: DU145_8.1

tag: cell line


title: H1_NPC_UTX

value: anti-FLAG M2 (Sigma-Aldrich, Catalog number M8823)


title: PREC_957E-AR_R1881_2

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description:
immortalized prostate epithelial cell
PREC/957E-AR cells cultured with 1nM R1881 for 24 hours and harvested

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.X software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Sequencing reads were mapped to the hg38 human genome build using TopHat v2.X and bowtie2 v2.2.X.
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.29
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package v1.14.1 using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: PrEC 957E/hTERT-AR

extract_protocol:
RNA was extracted using the Qiagen RNeasy Kit, (Qiagen Inc.), according to the manufacturer's protocol.  On-column DNase digestion was performed.  RNA concentration, purity, and integrity was assessed by NanoDrop (Thermo Fisher Scientific Inc) and Agilent Bioanalyzer.
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50 bp paired end reads.

treatment_protocol: Prostate cancer cell lines (LNCaP, VCaP, R1AD1, 22PC, and LAPC4) were cultured for 48 hours in their normal growth media (10% FBS) with vehicle (DMSO), 10nM R1881, or 10uM enzalutamide. After 48 hours, RNA was harvested. For PREC cells, cells were cultured with 1nM or ethanol vehicle for 24 hours and harvested.

value: PrEC 957E/hTERT-AR human immortalized prostate epithelial cell

tag: gender

value: male

value: PrEC 957E/hTERT-AR

tag: treatment

value: 1nM R1881 for 24 hours


title: dKO-NPC-BAF53B-rp1

description:
dKO-NPC-BAF53B-rp1
dKO-BAF53B-NPC.qval5.narrowPeak.gz

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptors were cut from reads using cutadapt (v1.13), and reads were aligned to human genome (UCSC hg38) using bowtie2 (v2.2.5).
Duplicates were removed using samtools (v1.3.1) and Picard Tools (v1.90). Signals were pileupped using MACS2 callpeak and bdgcmp, and differential open peaks were called using MACS2 bdgdiff
Signal density heatmap and profile were plotted using deeptools (v2.4.2), and motifs were found using homer.
Peaks were annotated with gene annotation using ChIPpeakAnno (v3.12.7) and gene ontology analysis was performed using clusterProfiler (v3.6.0).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: bed

extract_protocol:
In brief, 5×10^4 cells of each sample were processed for ATAC-seq.
DNA libraries were prepared for sequencing using standard Illumina protocols.

value: UTX and JMJD3 knockout


title: PREC_957E-AR_EtOH_2

description:
immortalized prostate epithelial cell
PREC/957E-AR cells cultured with ethanol vehicle for 24 hours and harvested

value: ethanol vehicle for 24 hours


title: PREC_957E-AR_R1881_1


title: dKO-NPC2-rp2

description:
dKO-NPC2-rp2
dKO-NPC2.qval5.narrowPeak.gz

value: human neural progenitor cells


title: dKO-NPC2-rp1

description:
dKO-NPC2-rp1
dKO-NPC2.qval5.narrowPeak.gz


title: H1-NPC2-rp2

description:
H1-NPC2-rp2
H1-NPC2.qval5.narrowPeak.gz

value: WT


title: H1-NPC2-rp1

description:
H1-NPC2-rp1
H1-NPC2.qval5.narrowPeak.gz


title: R1AD1_ENZA_2

description:
prostate cancer
R1AD1 cells cultured in 10% FBS with 10uM ENZ for 48 hours and harvested

value: R1AD1 human prostate tumor cell line

value: 10uM ENZ for 48 hours


title: R1AD1_R1881_2

description:
prostate cancer
R1AD1 cells cultured in 10% FBS with 10nM R1881 for 48 hours and harvested

value: 10nM R1881 for 48 hours


title: PREC_957E-AR_EtOH_1


title: DU145_8plus.1


title: DU145_8plus.3


title: R1AD1_ENZA_1


title: R1AD1_DMSO_2

description:
prostate cancer
R1AD1 cells cultured in 10% FBS with vehicle (DMSO) for 48 hours and harvested

value: vehicle (DMSO) for 48 hours


title: dKO-NPC-P4-2

first: qianyu

last: chen

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, reads were aligned to human genome (UCSC hg38) using HISAT2 (v2.0.4)
and gene expression was counted using samtools (v1.3.1) and htseq-count (v 0.6.0), filtered by a threshold of at least 20 averaged raw read counts among samples, and then normalized by GC-count and Gene-length using EDASeq (v2.12.0).
Differential expression and PCA plot were performed using DESeq (v 1.18.1) and genes with p-value < 0.05 and fold-change > 2 were considered as significant difference.
Correlation plot was performed using ggplot2 (v2.2.1) and heatmap was performed using pheatmap (v1.0.10).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: count

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line/strain

value: human neural progenitor cells with deletion of UTX and JMJD3


title: H1-NPC-P4-2


title: H1-NPC-P4-1


title: niPS_C2_Gel_R1

value: naive iPSCs


title: dKO-NPC-2


title: dKO-NPC-1


title: 22PC_ENZA_2

description:
prostate cancer
22PC cells cultured in 10% FBS with 10uM ENZ for 48 hours and harvested

value: 22PC human prostate tumor cell line


title: 22PC_ENZA_1


title: 22PC_R1881_2

description:
prostate cancer
22PC cells cultured in 10% FBS with 10nM R1881 for 48 hours and harvested


title: 22PC_R1881_1


title: dKO-D28-2

value: differentiated neural progenitor cells at day 28 with deletion of UTX and JMJD3


title: dKO-D28-1

source_name: differentiated neural progenitor cells at day 28


title: 22PC_DMSO_2

description:
prostate cancer
22PC cells cultured in 10% FBS with vehicle (DMSO) for 48 hours and harvested


title: H1-NPC-2


title: H1-NPC-1


title: 22PC_DMSO_1


title: R1AD1_R1881_1


title: dKO-NPC-P4-1


title: dKO-D28-INPUT

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were base-called and de-multiplexed using standard Illumina softwares. Bowtie2 was used to align the reads to the human genome hg38. Reads mapped to identical positions with same orientation in the genome were collapsed into one read.
The regions of H3K27me3 enrichment (peaks) were called using the SICER software package, with the input genomic DNA as a background control (parameters: W = 200; G = 600; FDR 0.01 cutoff applied).
Binding profiles and heatmaps were generated using ngsplot  and deeptools.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: bigwig

extract_protocol:
For  ChIP-seq, 1×107 cells of each sample were crosslinked in 1% formaldehyde with rotation for 10 minutes at room temperature. And then these crosslinked reactions were stopped by 0.125 M glycine with rotation for 5 minutes at room temperature. and cell sample were sonicated, and then ChIPed with H3K27me3 antibodies.
DNA libraries were prepared for sequencing using standard Illumina protocols.


title: dKO-NPC-INPUT


title: LAPC4_ENZA_1

description:
prostate cancer
LAPC4 cells cultured in 10% FBS with 10uM ENZ for 48 hours and harvested

value: LAPC4 human prostate tumor cell line


title: LAPC4_DMSO_2

description:
prostate cancer
LAPC4 cells cultured in 10% FBS with vehicle (DMSO) for 48 hours and harvested


title: LAPC4_R1881_2

description:
prostate cancer
LAPC4 cells cultured in 10% FBS with 10nM R1881 for 48 hours and harvested


title: R1AD1_DMSO_1


title: H1-D28-INPUT

value: differentiated neural progenitor cells at day 28


title: LAPC4_DMSO_1

value: male


title: VCAP_ENZA_2

description:
prostate cancer
VCAP cells cultured in 10% FBS with 10uM ENZ for 48 hours and harvested

source_name: VCaP

value: VCaP human prostate tumor cell line

value: VCaP


title: H1-NPC-INPUT


title: dKO_D28_H3K27me3

value: UTX and JMJD3 knockout


title: dKO_NPC_H3K27me3


title: VCAP_ENZA_1


title: H1_D28_H3K27me3


title: VCAP_R1881_2

description:
prostate cancer
VCAP cells cultured in 10% FBS with 10nM R1881 for 48 hours and harvested


title: VCAP_R1881_1


title: VCAP_DMSO_2

description:
prostate cancer
VCAP cells cultured in 10% FBS with vehicle (DMSO) for 48 hours and harvested


title: H1_NPC_H3K27me3


title: dKO-NPC-rp2

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptors were cut from reads using cutadapt (v1.13), and reads were aligned to human genome (UCSC hg38) using bowtie2 (v2.2.5).
Duplicates were removed using samtools (v1.3.1) and Picard Tools (v1.90). Signals were pileupped using MACS2 callpeak and bdgcmp, and differential open peaks were called using MACS2 bdgdiff
Signal density heatmap and profile were plotted using deeptools (v2.4.2), and motifs were found using homer.
Peaks were annotated with gene annotation using ChIPpeakAnno (v3.12.7) and gene ontology analysis was performed using clusterProfiler (v3.6.0).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: bigwig

extract_protocol:
In brief, 5×104 cells of each sample were processed for ATAC-seq.
DNA libraries were prepared for sequencing using standard Illumina protocols.


title: VCAP_DMSO_1


title: H1-D28-1


title: LAPC4_R1881_1


title: BSF_0272_HGLTNBBXX_1#X084_14_S19438

city: Vienna

first: Andreas

last: Bergthaler

address: Lazarettgasse 14 AKH BT25.3

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder.
Transcriptome analysis is performed using the Tuxedo suite. Reads are mapped on the mouse reference genome (Mus musculus, Ensembl e87, December 2016) using TopHat2 (v2.0.10).
Cufflinks (v2.2.1) is further used to assemble transcripts from spliced read alignments, using the Ensembl e87 transcriptome as the reference as well as de novo assembly of transcript models.
Differential expression is assessed with Cuffdiff (v2.2.1). Transcriptome sets of all replicates for each sample group will be combined with Cuffmerge.
Genome_build: Ensembl version e87(December 2016) of the Mus musculus genome.
Supplementary_files_format_and_content: tab-delimited text file of normalised cufflinks FPKM

extract_protocol:
Total RNA was extracted after sample homogenisation using Qiazol lysis reagent according to manufacturer's instructions.
RNA-seq libraries were prepared with TruSeq Stranded total mRNA ample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer).
Libraries will be pooled, diluted and sequenced on Illumina HiSeq 3000 using 50 bp single-read chemistry.

treatment_protocol: Mice were infected with 2x10^6 focal-forming units of  lymphocytic choriomeningitis virus (LCMV) clone 13 intravenously.

value: Liver


title: BSF_0272_HGLTNBBXX_1#X084_13_S19437


title: BSF_0272_HGLTNBBXX_1#X084_15_S19439


title: LAPC4_ENZA_2


title: H1-D28-2


title: dKO-NPC-rp1


title: BSF_0272_HGLTNBBXX_1#X084_11_S19435


title: LNCAP_ENZA_1

description:
prostate cancer
LNCAP cells cultured in 10% FBS with 10uM ENZ for 48 hours and harvested

source_name: LNCaP

value: LNCaP human prostate tumor cell line

value: LNCaP


title: BSF_0272_HGLTNBBXX_1#X084_12_S19436


title: LNCAP_ENZA_2


title: dKO-D28-rp2


title: BSF_0272_HGLTNBBXX_1#X084_8_S19433


title: BSF_0272_HGLTNBBXX_1#X084_9_S19434


title: dKO-D28-rp1


title: BSF_0272_HGLTNBBXX_1#X084_7_S19432


title: BSF_0272_HGLTNBBXX_1#X084_6_S19431


title: LNCAP_R1881_2

description:
prostate cancer
LNCAP cells cultured in 10% FBS with 10nM R1881 for 48 hours and harvested


title: H1-NPC-rp2

value: human neural progenitor cells

value: WT


title: BSF_0272_HGLTNBBXX_1#X084_4_S19430


title: LNCAP_R1881_1

value: 10nM R1881 for 48 hours


title: H1-NPC-rp1


title: LNCAP_DMSO_2

description:
prostate cancer
LNCAP cells cultured in 10% FBS with vehicle (DMSO) for 48 hours and harvested

value: vehicle (DMSO) for 48 hours


title: BSF_0272_HGLTNBBXX_1#X084_1_S19428


title: H1-D28-rp2


title: H1-D28-rp1


title: K562, U2AF1_S34F_Q157R.B

first: Robert

last: Bradley

address: 1100 Fairview Ave N

institute: Fred Hutch

data_processing:
Gene annotations from UCSC knownGene, Ensembl71, and MISO v2.0 were merged
Reads were mapped to the human genome (hg19) with bowtie and RSEM v1.2.4. RSEM was used to call Bowtie with option '-v 2'
Remaining reads were mapped to the genome with TopHat v2.1.1
Isoform ratios were quantified with MISO v2.0
For U2AF1_mutant-vs-WT comparisons, U2AF1_S34F_Q157R.B was compared to U2AF1_WT.B. All other U2AF1 mutant samples were compared to U2AF1_WT.A.
Genome_build: hg19
Supplementary_files_format_and_content: .txt files contain isoform ratio measurements (Psi) for splicing events with a minimum of 20 supporting reads. Splicing event types include cassette exons (se), mutually exclusive exons (mxe), competing 3' and 5' splice sites (a3ss, a5ss), and retained introns (ri).

growth_protocol: K562 cell lines were cultured in IMDM/10% FBS with penicillin (100 U/ml) and streptomycin (100 μg/ml)

extract_protocol:
RNA for RNA-seq was extracted with TRIzol (Thermo Fisher) according to manufacturer's protocols
RNA-seq libraries were prepared from TRIzol-isolated RNA using a modified protocol of the Illumina TruSeq RNA Library Prep Kit v2 (Illumina catalog no. RS-122-2001/2). After adapter ligation, AMPure XP beads were used to select  libraries between 100 and 400 bp. Libraries were amplified using 15 cycles of PCR and DNA fragments of 300 bp were purified after separation on a 2% agarose gel (Qiagen MinElute gel extraction kit).

treatment_protocol: K562 cells were transduced with lentivirus coding for WT or mutant forms of U2AF1 and SRSF2. Cells were sorted and expanded.

tag: lentiviral vector


title: K562, U2AF1_E159_M160insYE.A


title: LNCAP_DMSO_1


title: K562, U2AF1_Q157R.A


title: K562, U2AF1_R156Q.A


title: BSF_0272_HGLTNBBXX_1#X084_3_S19429


title: H3K9me3 ReChIP H3K14ac young

city: Charlottesville

first: Irina

middle: M.

last: Bochkis

state: Virginia

address: 1340 Jefferson Park Ave

department: Department of Pharmacology

institute: University of Virginia School of Medicine

description: chromatin immunoprecipitation

data_processing:
The reads were aligned to mouse genome (mm10; NCBI Build 38) using BWA (Li and Durbin, 2009). Duplicate reads were removed from the analysis. Reads (phred score > 30) that aligned uniquely were used for subsequent analysis.
Reads from two biological replicates were merged for each condition (Setd1 young, Setdb1 old, Kap1 young, Kap1 old, H3K4ac young, H3K14ac old). PeakSeq algorithm (Rozowsky et al., 2009) was used to identify bound peaks against input controls.
Genome_build: mm10
Supplementary_files_format_and_content: bed files with peak calls from PeakSeq with the following columns: chromosome, begin coordinate, end coordinate, enrichment, q-value

source_name: Liver

extract_protocol:
Snap-frozen mouse liver (100 mg) from wild type mice was used to prepare chromatin. Rabbit polyclonal antibodies specific to Setdb1 (Proteintech, 11231-1-AP),  Kap1 (Abcam, ab10483),  and anti-acetyl-histone-H3 specific to Lys-14 (Millipore, 07-353) were used for immunoprecipitation.
Libraries were prepared according to Illumina's instructions. Briefly, DNAs were blunted with a combination of T4 DNA polymerase, Klenow polymerase, and T4 PNK, then a single 3′-end “A” base was added using Klenow exo (3′-to-5′ exo minus). multiplex adapters were then ligated to the ends of the modified DNA.  After adapter ligation DNA was PCR amplified with Broad custom primers for 16 cycles and library fragments of ~280 bp (~150-bp mononucleosome insert plus ~130-bp adaptor and PCR primer sequences) were  isolated using Pippin Prep agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 (Sedb1 & Kap1) and Illumina Hiseq 2500 (H3K14ac)  following the manufacturer's protocols.

tag: strain

tag: age

value: 3 months


title: H3K9me3 ReChIP H3K14ac old

description: chromatin immunoprecipitation

value: 21 months


title: K562, U2AF1_R156H.A

tag: genotype


title: H3K14ac ReChIP H3K9me3 old

description: chromatin immunoprecipitation


title: H3K14ac ReChIP H3K9me3 young

description: chromatin immunoprecipitation


title: H3K14ac old rep3

description: chromatin immunoprecipitation


title: K562, U2AF1_S34F.A


title: H3K14ac old rep2

description: chromatin immunoprecipitation


title: K562, U2AF1_I24V.A


title: H3K14ac old rep1

description: chromatin immunoprecipitation


title: dKO-NPC-BAF53B-rp2

description:
dKO-NPC-BAF53B-rp2
dKO-BAF53B-NPC.qval5.narrowPeak.gz


title: K562, U2AF1_I24T.A


title: H3K14ac young rep3

description: chromatin immunoprecipitation


title: H3K14ac young rep2

description: chromatin immunoprecipitation


title: K562, U2AF1_WT.B


title: K562, U2AF1_WT.A


title: K562, SRSF2_H99L


title: H3K14ac young rep1

description: chromatin immunoprecipitation


title: K562, SRSF2_P107H


title: Setdb1 old rep2

description: chromatin immunoprecipitation


title: K562, SRSF2_P95_R102del_P107H


title: Setdb1 old rep3

description: chromatin immunoprecipitation


title: genomic DNA from peripheral blood from ST13

type: genomic

city: Irapuato

first: Gertrud

last: Lund

state: Guanajuato

address: Km 9.6 del Libramiento Norte Carretera Irapuato-León SN

department: Genetic Engineering

country: Mexico

institute: CINVESTAV Irapuato

description:
Postprandial day sample
ST13

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing: The IDAT files were normalized (control normalization) and background corrected using the methylation module (1.9.0) available on GenomeStudio (v2011.1) software from Illumina. DNA methylation data were obtained for 865,919 probes. 110,139 SNP-related probes (Pidsley et al. Genome Biology 2016;17:208) were remove prior to any analysis. All samples probes were filtered away for further analysis based on a detection P-value > 0.01. Approximately 0.8% (6,691/859,169) of the probes were removed due not matching the filtering criteria.

label: Cy5 and Cy3

source_name: Pheriferical Blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was quantified by nanodrop and 500ng of DNA from each sample was bisulfite converted using the Zymo EZ DNA Methylation Kit (Zymo Research, Irvine, CA USA) following the manufacturer’s protocol using the specified modifications for the Illumina Infinium Methylation Assay. Converted DNA was processed through the EPIC array protocol. Later, array beadchips were scanned on the Illumina HiSeq2000 platform. DNA methylome was captured by HumanMethylationEPIC (EPIC) BeadChip (Illumina, CA, USA) using the manufacturer’s standard protocol.

treatment_protocol: Five consecutive, same-day blood samples were obtained from a total of 12 subjects -with different BMI- in two prandial conditions: fasting (FD) and post-prandial (PD) with hypercaloric meal.

value: Male

tag: bmi

value: Normal

tag: metabolic state

value: Postprandial


title: genomic DNA from peripheral blood from VS22

description:
Postprandial day sample
VS22

value: Obese


title: genomic DNA from peripheral blood from RL17

description:
Postprandial day sample
RL17

value: Overweight


title: genomic DNA from peripheral blood from TR14

description:
Postprandial day sample
TR14


title: K562, SRSF2_P95_R102del


title: genomic DNA from peripheral blood from JM7

description:
Fasting day sample
JM7

value: Fasting


title: genomic DNA from peripheral blood from RR23

description:
Postprandial day sample
RR23


title: genomic DNA from post-mortem hippocampus 63

city: Houston

first: Gabriel

middle: Rodrigo

last: Fries

state: TX

address: 1941 East Rd, Suite 5102A

department: Psychiatry

institute: University of Texas Health Science Center

hyb_protocol: Standard Illumina Infinium hybridization protocol.

scan_protocol: Standard Illumina Infinium scan protocol. Scan performed on iScan microarray reader.

data_processing:
Raw data were uploaded to GenomeStudio (Illumina) and background-corrected.
Unmethylated and methylated signal intensities in Series supplementary file

label: Cy3 and Cy5

label_protocol: Standard Illumina Infinium protocol.

extract_protocol: DNA was isolated from frozen hippocampal tissue using a modified protocol at the HBCC-NIMH. Briefly, pulverized hippocampal tissues were lysed in PureGene lysis solution (Qiagen, Hilden, Germany) containing proteinase K at 55º C overnight, followed by incubation with RNAse at room temperature for 15 minutes. After centrifugation at 14,000 rpm for 1 hour at 4º C and transfer of the supernatant to a new microtube, the DNA was precipitated by addition of cold isopropyl alcohol and further centrifugation at 14,000 rpm for 30 minutes. After a washing step with 90% ethanol and a final centrifugation at 14,000 rpm for 20 minutes, the pellet was air-dried and resuspended in TE buffer.

tag: Sex

tag: group

value: Control

tag: age at death

tag: race

value: Caucasian

value: post-mortem interval:21.5

tag: tissue ph

value: post-mortem hippocampus


title: genomic DNA from peripheral blood from JP20

description:
Postprandial day sample
JP20


title: genomic DNA from peripheral blood from MG21

description:
Postprandial day sample
MG21


title: genomic DNA from peripheral blood from RA24

description:
Postprandial day sample
RA24


title: genomic DNA from peripheral blood from VM3

description:
Fasting day sample
VM3


title: Setdb1 young rep3

description: chromatin immunoprecipitation

tag: tissue

value: Liver


title: genomic DNA from peripheral blood from RR11

description:
Fasting day sample
RR11


title: genomic DNA from peripheral blood from MG9

description:
Fasting day sample
MG9


title: genomic DNA from peripheral blood from MH18

description:
Postprandial day sample
MH18


title: K562, SRSF2_P95H


title: genomic DNA from post-mortem hippocampus 64

value: Female

value: Bipolar

value: post-mortem interval:29.5


title: genomic DNA from peripheral blood from VS10

description:
Fasting day sample
VS10


title: genomic DNA from peripheral blood from GA4

description:
Fasting day sample
GA4


title: genomic DNA from peripheral blood from JM19

description:
Postprandial day sample
JM19


title: genomic DNA from post-mortem hippocampus 62

value: post-mortem interval:18.5


title: Setdb1 young rep2

description: chromatin immunoprecipitation

value: 3 months


title: genomic DNA from peripheral blood from RA12

description:
Fasting day sample
RA12


title: genomic DNA from peripheral blood from TR2

description:
Fasting day sample
TR2


title: Setdb1 young rep1

description: chromatin immunoprecipitation


title: genomic DNA from peripheral blood from JP8

description:
Fasting day sample
JP8


title: genomic DNA from peripheral blood from GA16

description:
Postprandial day sample
GA16


title: K562, SRSF2_R86_G93dup


title: K562, SRSF2_S54F


title: genomic DNA from peripheral blood from MH6

description:
Fasting day sample
MH6


title: Kap1 old rep2

description: chromatin immunoprecipitation

value: 21 months


title: Kap1 old rep1

description: chromatin immunoprecipitation


title: genomic DNA from post-mortem hippocampus 61

value: Male

value: post-mortem interval:18


title: Kap1 young rep2

description: chromatin immunoprecipitation


title: genomic DNA from post-mortem hippocampus 60

value: post-mortem interval:43.5


title: K562, SRSF2_WT


title: Kap1 young rep1

description: chromatin immunoprecipitation


title: genomic DNA from peripheral blood from VM15

description:
Postprandial day sample
VM15

value: Normal

value: Postprandial


title: mpPHH-5

city: New York

first: Inna

last: Ricardo-Lax

address: 1230 york avenue

institute: Rockefeller University

data_processing:
Alignment: Fastq files were processed with kallisto on an index built from Ensembl release hg38_rel85 trancripts;  kallisto -b 60 -l 28 -s 14; pachterlab.github.io/kallisto/
Expression testing: kallisto output was processed with sleuth for expression testing between cryopreserved and mouse-passaged samples; http://pachterlab.github.io/sleuth/
Transcript with highest mean expression across all sample was selected as representative per gene.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes sleuth output, gene symbol, and pseudocount matrix per sample

extract_protocol:
RNA was extracted from tissue using Trizol and Rneasy (Qiagen)
Stranded RNAseq libraries were prepared from 250ng of total RNA using standard Illumina protocols with Poly-A selection

treatment_protocol: For Cryo-preserved PHH, Tryzol was added directly to cells from the cryovial. For mpPHH, Hepatocytes were isolated from chimeric livers: Briefly, mice were anesthetized with ketamine/xylazine and a 24G angiocath was inserted into the inferior vena cava. Then the portal vein was cut, and the mouse liver was perfused sequentially with PBS-/- supplemented with heparin, Hanks buffered saline solution (HBSS) supplemented with 5 mM EDTA and 50 mM HEPES, and finally HBSS supplemented with 0.05% Type IV collagenase (Sigma Aldrich) and 1 U/ml DNAse (Thermo Fisher, Waltham, MA). After digestion the liver was disrupted over a 70 μm cell strainer, the cell suspension (50 ml) was spun at 50xg for 5 min at 4oC using an Allegra X-14R Centrifuge (Beckman Coulter, Indianapolis, IN). The supernatant was gently aspirated and the cells were washed once with PBS-/-. The cell pellet was resuspended in 10 ml PBS-/- and gently mixed with equal volume of Percoll working solution (catalog number 17-0891-01, GE Healthcare, Uppsala, Sweden). Percoll working solution consisted of 5.4% 10x PBS-/-, 48.6% Percoll, and 46% William’s E medium (catalog number 12551-032, Life technologies, Grand Island, NY). The cell suspension was spun at 100xg for 5 min at 4 oC and the pellet washed once with PBS. After centrifugation at 50xg the cells were resuspended in PBS and left on ice for 45 min. Then a second round of Percoll was used to further purify the cell suspension. Cells were lyzed in Trizol and frozen in -80oC.

tag: mouse passaged

value: mpPHH

tag: mouse id

tag: cell type

value: mouse passaged primary human hepatocytes


title: genomic DNA from peripheral blood from RL5

description:
Fasting day sample
RL5

tag: gender

value: Overweight

value: Fasting


title: Netrin_H3K4me3 ChIP-seq rep3

first: Fabrice

last: Lavial

address: 28 rue Laennec

institute: CRCL

data_processing:
BWA was used for alignment of data to the mm9 genome with de-duplication performed using Picard tools, followed by peak calling using macs2 with narrow peak settings. To compare between control and netrin-1 conditions, homer annotatePeaks.pl was used with size = 2000, hist = 10 and –ghist used to generate read enrichments from both the control and netrin-1 sample using the control macs2 peaks. Data was then plotted in R using custom scripts
Genome_build: mm9
Supplementary_files_format_and_content: Coverage files used to plot the density composites for bivalent genes in figure 3k. Both for H3K27me3 and H3K4me3. Both text files output from Homer AnnotatePeaks after creating tag directories with the bam files.

growth_protocol: mESC are grown in serum/LIF conditions

extract_protocol: ChIP-seq is performed as previously described (Galonska et al., Cell Stem cell 2015)

treatment_protocol: mESC are stably transfected with ppy-cagg-ires-puro vector epty or encoding a netrin-1 transgene.

value: Embryonic stem cells

tag: genotype/variation

value: exogenously expressing netrin-1

tag: chip antibody

tag: chip antibody info.

value: Active Motif #61379


title: Setdb1 old rep1

description: chromatin immunoprecipitation

tag: strain

value: Liver

tag: age


title: genomic DNA from peripheral blood from ST1

description:
Fasting day sample
ST1

tag: bmi


title: Netrin_H3K4me3 ChIP-seq rep2


title: mpPHH-3


title: mpPHH-4


title: Netrin_H3K4me3 ChIP-seq rep1


title: mpPHH-2


title: genomic DNA from post-mortem hippocampus 59

value: Female

value: Control

value: Other

value: post-mortem interval:48

value: post-mortem hippocampus


title: WT_H3K4me3 ChIP-seq rep3

value: vector control


title: mpPHH-1


title: genomic DNA from post-mortem hippocampus 58

value: Caucasian

value: post-mortem interval:22


title: WT_H3K4me3 ChIP-seq rep2


title: K562, SRSF2_S54A

tag: cell line

tag: lentiviral vector

tag: genotype


title: Cryopreserved PHH1

value: Cryo

value: cryopreserved commercial primary human hepatocytes


title: WT_H3K4me3 ChIP-seq rep1


title: genomic DNA from post-mortem hippocampus 54

tag: Sex

tag: group

value: Bipolar

tag: age at death

value: post-mortem interval:65.5


title: genomic DNA from post-mortem hippocampus 55

tag: race

tag: tissue

value: post-mortem interval:21

tag: tissue ph


title: Cryopreserved PHH2

tag: mouse passaged

tag: mouse id

tag: cell type


title: K562, SRSF2_R94_P95insR


title: genomic DNA from post-mortem hippocampus 53

value: post-mortem interval:54


title: genomic DNA from post-mortem hippocampus 52

value: Male

value: post-mortem interval:37.5


title: genomic DNA from post-mortem hippocampus 56

value: post-mortem interval:33.5


title: genomic DNA from post-mortem hippocampus 51

value: post-mortem interval:47


title: PC1_Rep1

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Raw sequence reads were trimmed to remove poor quality reads, adapter contamination, and the first 6 base pairs, using Trim Galore (v0.6.1, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The remaining sequences were mapped using Bismark (v0.21.0) (Krueger and Andrews, 2011) to the human reference genome GRCh37 in paired-end mode. CpG methylation calls were extracted and analysed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCh37
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: iPSC

extract_protocol:
DNA was purified from cell lysates and then used for library construction
Whole-genome bisulfite libraries were prepared using a post-bisulfite adaptor tagging (PBAT) strategy as previously described (Smallwood, et al. (2014). Nature Methods 11, 817–820), with some modifications. Bisulfite conversion was performed on cell lysates using the Imprint Zymo direct kit. After purification, 1st strand synthesis was performed using 6N-forward oligos for 37°C for 30min. Subsequently, samples were treated with Exonuclease I for 1hr at 37°C, and DNA was purified using AMPure XP beads (Agencourt). Samples were eluted in 2nd strand synthesis mix with 6N-reverse oligo and incubated at 37°C for 90min. DNA was purified and amplified with KAPA HiFi HotStart DNA Polymerase (KAPA Biosystems). The amplified libraries were purified and assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyzer
post-bisulfite adaptor tagging (PBAT)

tag: background strain

value: Wild-type

value: iPSC

value: conventional


title: genomic DNA from post-mortem hippocampus 49

value: Control

value: post-mortem interval:23.5

value: post-mortem hippocampus


title: genomic DNA from post-mortem hippocampus 44

value: Female

value: Other

value: post-mortem interval:36.5


title: Netrin_H3K27me3 ChIP-seq rep3

value: Embryonic stem cells

tag: genotype/variation

value: exogenously expressing netrin-1

tag: chip antibody

tag: chip antibody info.


title: genomic DNA from post-mortem hippocampus 45

value: Caucasian

value: post-mortem interval:40


title: genomic DNA from post-mortem hippocampus 47

value: Bipolar

value: post-mortem interval:31


title: niPSC5_Rep1

value: naive


title: PC1_Rep2


title: genomic DNA from post-mortem hippocampus 41

value: Male

value: post-mortem interval:51


title: Netrin_H3K27me3 ChIP-seq rep2


title: genomic DNA from post-mortem hippocampus 46

value: post-mortem interval:24


title: genomic DNA from post-mortem hippocampus 48

value: post-mortem interval:24.5


title: niPSC6_Rep2

value: Wild-type

value: iPSC


title: genomic DNA from post-mortem hippocampus 39

value: post-mortem interval:27

value: post-mortem hippocampus


title: genomic DNA from post-mortem hippocampus 36

value: Control

value: post-mortem interval:46.5


title: genomic DNA from post-mortem hippocampus 37

value: post-mortem interval:31.5


title: genomic DNA from post-mortem hippocampus 42

value: post-mortem interval:44.5