title: RNA sequencing of FACS purified HFSCs, total epidermal cells and cultured HFSCs

city: Münster

first: Sara

middle: A

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

institute: Max Planck Institute for Molecular Biomedicine

summary: We sequenced mRNA from HFSCs that were FACS purified (CD34+alpha-6 Integrin+ cells) from p21 mouse epidermis, total epidermal cells from p21 mice and HFSCs cultured for 14 days in 3C cultures, 3 biological replicates each. We sequenced mRNA from different cell populations that were FACS-purified from HFSC cultures (also known as 3C cultures), 3 biological replicates each. We performed two independent comparisons: 1. Comparison of FACS-purified cells grown in standard 3C cultures: HFSCs (CD34+ alpha-6 Integrin+) and non-HFSCs (CD34neg alpha-6 Integrin+). 2. Comparison of total cells in 3C cultures treated for 48 hours with dorsomorphin (BMP inhibitor that causes depletion of CD34+ alpha-6 integrin+ cells in 3C cultures) or with cyclopamine Shh inhibitor that causes enrichment of CD34+ alpha-6 integrin+ cells in 3C cultures).

overall_design: Examination of transcriptomes from bona fide HFSCs, total epidermal cells and cultured HFSCs. The aim of the experiment was to determine: for the first comparison (1.) the identity of the two populations of cells that grow in 3C cultures (CD34+ alpha-6 Integrin+ and CD34neg alpha-6 Integrin+); and for the second comparison (2.) the early transcriptional changes that lead to a fate change in cells grown in 3C cultutres to drive depletion (with dorsomorphin treatment) or enrichment (with cyclopamine treatment) of HFSCs.

first: Carlos

last: Chacón-Martínez


title: Transcriptome dynamics during the development of heart failure caused by mitochondrial complex I dysfunction and pressure overload

status: Public on Dec 09 2016

city: Philadelphia

first: Long

last: Gao

state: PA

address: 4002 Colket Translational Research Building (CTRB) 3501 Civic Center Boulevard

country: USA

institute: The Children’s Hospital of Philadelphia

type: Expression profiling by high throughput sequencing

summary: Comprehensive knowledge of the dynamic changes in the cardiac transciptome can inform disease mechanism. Previous transcriptome profiling studies on heart failure rely on either microarray or RNA-Seq with low coverage, leaving a large portion of the transcriptome unexplored. Additionally, previous studies only examined two end stages of the disease, onset and late-stage heart failure. Profile of the transcriptome in the middle stage of disease progression can reveal critical molecular events underlying disease transition. Towards these goals, we conducted a multi-factorial RNA-Seq experiment, comparing the dynamic changes in the transcriptome of two murine models of heart failure, pressure overload and loss of mitochondrial complex I.  Our data represents the deepest transcriptome coverage to date, covering onset, progression, and late stage of the disease. We found extensive differences in the expression magnitude and dynamics of the transciptomes in different heart failure models. In addition, such differences are associated with progressive worsening of cardiac physiology. Our analysis revealed that mitochondrial dysfunction combined with stress leads to increased number of differentially expressed long intergenic noncoding RNAs, including a recently identified lincRNA that is a master regulator of the cardiac lineage during development.

overall_design: Cardiac tissues were cleaned with PBS and harvested at 1, 2, 4, and 8 weeks after surgeries by freezing in liquid nitrogen. Cardiac RNA profiles of wild type (WT) and ndufs4H-/- mice after surgeries were generated by deep sequencing at 4 time points, in quadruplicate, using Illumina HiSeq2000. The three factors of the data are genetic (WT vs. ndufs4H-/-), environmental stress (trans-aortic constriction vs. Sham controls), and time (Week 1, Week 2, Week 4 and Week 8). Thus, there are 16 samples in total and each sample has 4 replicates.

first: Chi

middle: F

last: Lee

first: Xiaoke

last: Ma

first: Peng

first: Lindsey

last: Gifford

first: Georgios

last: Karamanlidis

first: Lorena

last: Menendez

first: Rong

last: Tian

first: Kai

last: Tan


title: A permissive chromatin state regulated by ZFP281-AFF3 in controlling the imprinted Meg3 polycistron

status: Public on Dec 08 2016

city: Nanjing

first: Chengqi

last: Lin

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

country: China

institute: Southeast University

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Genomic imprinting is an epigenetic regulation which leads to gene expression in a parent-of-origin specific manner. Previously we have demonstrated that AFF3, the central component of Super Elongation Complex-like 3 (SEC-L3), can specifically bind both the intergenic differentially methylated region (IG-DMR) and the enhancer within the imprinted Dlk1-Dio3 locus to regulate the expression of the Meg3 polycistron. However, the mechanism underlying how AFF3 can interact with distinct chromatin regulatory elements remains unknown. Here, we demonstrate that AFF3 is associated with the Krüppel-like zinc finger protein ZFP281. ZFP281 is required for the recruitment of AFF3 to the enhancer and regulates the allele-specific expression of the Meg3 polycistron in mouse embryonic stem (ES) cells at the transcriptional elongation level. Our genome-wide analyses further identify ZFP281 as a critical factor generally associating with AFF3 at enhancers and functioning together with AFF3 in regulating the expression of a subset of gene. Our study suggests that different zinc finger proteins can function as molecular switchers to regulate the context-dependent function of AFF3 and set a balanced chromatin state for maintaining the allele specific expression pattern of the imprinted Dlk1-Dio3 locus.

PLEASE BE AWARE THAT THE SUBMITTER REQUESTED DELETION OF BIGWIG AND PEAK-CALL FILES POST-PUBLICATION. PLEASE CONTACT SUBMITTER FOR FURTHER INFORMATION.

overall_design: ChIP-seq of ZFP281 in mES cells. ChIP-seq of Pol II and AFF3 in mES cells after ZFP281 shRNA and non-targeting shRNA. ChIP-seq of ZFP281 in ZFP57 WT and KO ES cells. RNA-seq of mES cells after ZFP281 shRNA and non-targeting shRNA.

first: Yang

last: Shen


title: Transcriptomic profiling discloses molecular and cellular events related to neuronal differentiation in SH-SY5Y cells

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

summary: Human SH-SY5Y neuroblastoma cells are widely utilized in in vitro studies to dissect out pathogenetic mechanisms of neurodegenerative disorders. These cells are considered as neuronal precursors and differentiate into more mature neuronal phenotypes under selected growth conditions. In this study, we performed systematic transcriptomic (RNA-seq) and bioinformatic analysis to pinpoint pathways and cellular processes underlying neuronal differentiation of SH-SY5Y cells according to a two-step paradigm: retinoic acid treatment followed by enriched neurobasal medium. Categorization of 1989 differentially expressed genes (DEGs) identified in differentiated cells outlined meaningful biological functions associated with changes in cell morphology including remodelling of plasma membrane and cytoskeleton, neuritogenesis. Seventy-three DEGs were assigned to Axonal Guidance Signalling pathway, and the expression of selected gene products such as neurotrophin receptors, the functionally related SLITRK6, and semaphorins, was validated by immunoblotting. Along with these findings, the differentiated cells exhibited the ability to elongate longer axonal process as assessed by the morphometric evaluation. Recognition of molecular events occurring in differentiated SH-SY5Y cells is necessary to accurately interpret the cellular responses to specific stimuli in studies on disease pathogenesis.

overall_design: Comparison of cell line SH-SY5Y differentiated and undifferentiated.

first: Francesco

last: Pezzini

first: Laura

last: Bettinetti

first: Francesca

last: Di Leva

first: Marzia

last: Bianchi

first: Elisa

last: Zoratti

first: Rosalba

last: Carrozzo

first: Filippo

middle: M

last: Santorelli

first: Massimo

last: Delledonne

first: Maciej

last: Lalowski

first: Alessandro

last: Simonati


title: Transcriptomic signatures uncover gene expression differences associated with the development of phenotypic differences in serial organs

city: Lyon

first: Marie

last: Semon

address: 46, allée d’Italie

department: Biologie

country: France

institute: ENS de Lyon

summary: Gene expression differences during development provide the basis for adult phenotypic differences. This is true between species, but also between organs of the same type, yet with different shapes, within the same organism. In such “serial organs”, current models state that organ identity is initially provided by a few specifically expressed genes (e.g. homeotic genes) that initiate differential regulation in an otherwise common developmental program. We know surprisingly little about the nature and structure of expression differences later during organ morphogenesis in relation to organ identity. Better understanding this would provide insights to how differences in gene expression during development ultimately result in organs that are similar, yet different. To address this question, we focused on the morphogenesis of two well-differentiated serial appendages, the upper and lower first molars in mouse. We analyzed tight RNA-seq transcriptome timeseries taken in their entirety with a set of purposely developed bioinformatic tools and complementary bench data. In line with expectations, we found that the two teeth share most of the temporal dynamics in gene expression despite heterochronies, which defines a core developmental program for making a molar. We found, surprisingly, just one specifically expressed gene but evidenced a small set of biased genes (enriched for transcription factors), constantly biased ever since the specification of lower and upper jaw. This argues for quantitative differences in gene expression modulating the core program, on top of the recognized qualitative bias (specific genes). Moreover, two findings stand against two common assumptions in comparative developmental gene expression: 1) that gene expression differences should mainly be of regulatory origin as we evidence that pervasive expression differences between lower and upper molar germ are at least in part due to a difference in the relative quantity of mesenchyme with no further need for intracellular differences in regulation; 2) that gene expression differences should increase with time as embryos/organs progress in differentiation (funnel pattern) as we demonstrate an early peak of difference (inverted hourglass pattern), when developmental processes are transiently most different. Finally our findings enable us to draw up a scenario of how the upper molar makes an additional row of cusps. More generally, our study shows that cellular proportions largely shape whole organ transcriptomes and are also responsible for transcriptomic heterochronies, which will be of interest for the understanding of gene expression evolution.

overall_design: In this study, we targeted the period of lower and upper molar development during which most of the crown morphogenesis, and notably cusp patterning, happens. For eight consecutive stages each separated by 12 hours, we sampled lower and upper first molar tooth germs, each time from a single individual.

last: Sémon

first: Sophie

last: Pantalacci


title: Single cell RNA sequencing of primary breast cancer.

city: Seoul

first: Woosung

last: Chung

state: State...

address: Samsung Medical Center

country: South Korea

institute: Samsung Genome Institute

summary: We performed single cell RNA sequencing (RNA-seq) for 549 primary breast cancer cells and lymph node metastases from 11 patients with distinct molecular subtypes (BC01-BC02, estrogen receptor positive (ER+); BC03, double positive (ER+ and HER2+); BC03LN, lymph node metastasis of BC03; BC04-BC06, human epidermal growth factor receptor 2 positive (HER2+); BC07-BC11, triple-negative breast cancer (TNBC); BC07LN, lymph node metastasis of BC07) and matched bulk tumors. We separated these single cells into epithelial tumor and tumor-infiltrating immune cells using inferred CNVs from RNA-seq. The refined single cell profiles for the tumor and immune cells provide key expression signatures of breast cancer and the surrounding microenvironment.

overall_design: All single-cell mRNA expression profiles were acquired from eleven patients (BC01-BC11) including two lymph node metastases (BC03LN, BC07LN) (549 samples). We applied four filtering criteria so as to remove samples with low sequencing quality and finally obtained 515 single cell sequencing data. Matched bulk tumor tissues and/or pooled cells were also sequenced and analyzed by the single cell RNA-seq pipeline (14 samples). Bulk tumor transcriptomes showed significant correlations with the average of single cell transcriptomes.

first: W

first: H

middle: H

last: Eum

last: Lee

last: Han

last: Park


title: Global Deletion of TSPO Does Not Affect the Viability and Gene Expression Profile.

city: Beijing

first: Jianmin

last: Zhang

state: Beijing

address: 5# Dong Dan San Tiao

department: Immunology

institute: Peking Union Medical College

summary: Translocator Protein (18kDa, TSPO) is a mitochondria outer membrane transmembrane protein and which expression is elevated during inflammation and injury. However, the exact function of TSPO is still controversial. Here, we constructed TSPO global knockout (KO) mice by Cre-LoxP system independently, which abolished TSPO protein expression in all tissues and shown normal phenotypes. The birth rate of TSPO heterozygote (Het)/Het breeding was consistent with the Mendel’s Law, suggesting a normal viability of TSPO KO mice at birth. RNAseq analysis showed no significant difference in the gene expression profile of lung tissues from TSPO KO mice compared with that of wild type mice, even the genes associated with bronchial alveoli immune homeostasis. The alveolar macrophage population was also not affected by TSPO deletion in the physiological condition. Our findings contradicts the results of Papadopoulos, but confirmed Selvaraj’s findings. This study reveals TSPO deficiency does not affect the viability and bronchial alveoli immune homeostasis.

overall_design: Lung tissue mRNA profiles of wild type (WT) and TSPO knockout (KO) mice were generated by deep sequencing using Illumina’s digital gene expression tag profiling (DGE) system, in triplicate. Every lung tissue RNA samples [WT (D,H,Z) and KO (B,F,M)] were pooled from three tissue samples of littermates.

first: Huaishan

last: Wang

first: Kangle

last: Zhai

first: Yingchao

last: Xue

first: Jia

last: Yang

first: Qi

first: Yi

last: Fu

first: Yu

last: Hu

first: Fang

last: Liu

first: Weiqing

first: Lianxian

last: Cui

first: Hui

last: Chen

first: Wei

last: He


title: Establishment of monkey imprinted differentially methylated regions map by comparative analysis of parthenogenetic haploid embryonic stem cells and sperms

city: Kunming

first: Tao

last: Tan

address: No. 1 Boda Road, Yuhua Area, Chenggong District, Kunming, Yunnan,

institute: Primate Translational Medicine Research Center, Kunming University of Science and Technology

type: Methylation profiling by high throughput sequencing

summary: Genomic imprinting is a important biological process, which leads to parental specific gene expressions. Improper gene imprinting results in several developmental abnormalities, cancer and other diseases. Studies in mice indicated genomic imprinting establishment relied on parental allele-specific DNA methylation during gametogenesis. Despite the fact that genomic imprinting is highly conserved in mammalian, the species specific pattern exists. Until now, except that of in mouse, informations about imprinting patterns is little, especially in primates.     Through generation genome-wide 5mC and 5hmC profiles for two types of haploid genomes from rhesus monkeys, including parthenogenetic haploid ESCs ( PG ha ESCs) (derived from rhesus monkey parthenogenetic embryos) and sperms. We clearly characterized and distinguished methylome (5mC) from hydroxymethylome (5hmC)(which can not discriminate from methylome in traditional bisulfite (BS) sequencing) in haploid genomes. Based on these information, we determined distribution patterns of 5mC and 5hmC in ha ESCs and sperms. Interestingly,      both 5hmC levels and distribution patterns were similar in ha ESCs and sperms, and 5hmC  which is enriched in the regions with low 5mC frequency. Meanwhile through comparing DNA methylation and hydroxymethylation status between sperms and ha ESCs, we first provided a fundamental information of monkey imprinted differentially methylated regions (DMRs) distribution in monkey chromosomes. Second, we observed that DMRs did not overlap with hydroxymethylated regions (DMR or DhMR), suggesting that establishment of imprinted regions was not interfered by 5hmC. Our results demonstrate DNA methylation profiling of PG ha ESCs and sperms can be uesed as a powerful and effective method to map and characterize imprinted regions in non-human primates genome.

overall_design: DNA methylation sequencing of monkey ha ESCs and sperms

first: Yudong

last: Xia

first: Fei

last: Gao


title: Effect of monocrotophos on gut metatranscriptome

status: Public on Dec 07 2016

city: Madurai

first: Velmurugan

last: Ganesan

state: Tamilnadu

address: Palkalainagar

department: Department of Molecular Biology, School of Biological Sciences

country: India

institute: Madurai Kamaraj University

summary:
Purpose: To study the differential expression of gut bacterial mRNAs during chronic organophosphate treatment.
Methods: Balb/c mice were treated with organophosphate (monocrotophos 28 ug/kg body weight/day) directly in drinking water for 180 days. Glucose tolerance tests indicated the induction of glucose intolerance. The total RNA was isolated by using TRIZOL from the cecal tissue that is cleared off fecal contents and subsequently the eukaryotic and bacterial rRNAs were removed by using MicrobExpress and MicrobEnrich kits (Ambion).  Subsequently, RNA library was contructed using illumina kit as per manufacturer's instructions.
Results: The reads were annotated to the reference human gut microbiome database and we found differential expression of large number of genes especially those involved in organophosphate degradation. Our subsequent studies proved that gut microbial degradation of organophosphates induces glucose intolerance via gluconeogenesis.
Conclusions: Chronic organophosphate-induced hyperglycemia is mediated by the organosphosphate-degrading potential of gut microbiota.

overall_design: mRNA profile of gut bacteria was generated by deep sequencing using Illumina HiSeq 1000

first: Ganesan

last: Velmurugan

first: Subbiah

last: Ramasamy


title: DNase-seq from adipocyte (ENCSR998KYQ)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Cell density, Her2 and progesterone signaling regulate dissemination of breast cancer cells

city: Regensburg

first: Christoph

middle: Andreas

last: Klein

state: Bavaria

address: Franz-Josef-Strauß-Allee 11

department: Experimental Medicine and Therapy Research

country: Germany

institute: University of Regensburg

type: Non-coding RNA profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Cell density, Her2 and progesterone signaling regulate dissemination of breast cancer cells [miRNA-Seq]

summary: Disseminated breast cancer cells display genotypes disparate from the predominant clone of the primary tumor before manifestation of metastasis, suggesting that cancer cell dissemination occurs preferentially early; however, the underlying molecular mechanisms are unknown. Investigating metastasis in a Her2-driven mouse model, we found that the progesterone-induced paracrine cytokines Wnt4 and Rankl induced migration and early dissemination shortly after Her2 activation. Once tumorigenic growth was established, progesterone receptor (PgR) expression was lost and Wnt4/Rankl induced proliferation. The altered response from migration to proliferation was determined by cell density involving miRNA-regulated PgR expression and was reversible. Cells from early, low-density lesions displayed more functional stemness traits than cells from dense, advanced tumors, migrated more and founded significantly more metastases. The data suggest that many metastases are derived from early-disseminated cancer cells, implying that our concepts for systemic therapy need to be revised.

overall_design: We analysed miRNA expression in the Her2 expressing cell lines as well as the secreting miRNA containing particles to find out PgR regulating miRNAs

first: Hedayatollah

last: Hosseini

first: Martin

last: Hoffmann

first: Gunter

last: Meister


title: Single Cell RNA-Sequencing Identifies Diverse Roles of Epithelial Cells in Idiopathic Pulmonary Fibrosis

city: Los Angeles

first: Jie

last: Tang

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

summary: Idiopathic pulmonary fibrosis (IPF) is a lethal interstitial lung disease causing alveolar remodeling, inflammation, and fibrosis.  We utilized single cell RNA-sequencing (scRNA-Seq) to identify epithelial cell types and associated biological processes involved in the pathogenesis of IPF.  Transcriptomic analysis of epithelial cells from normal human lung defined gene expression patterns associated with highly differentiated alveolar type 2 (AT2) cells, indicated by enrichment of RNAs critical for surfactant homeostasis.  In contrast, scRNA-seq of IPF cells identified three distinct subsets of epithelial cell types with characteristics of conducting airway basal and goblet cells and, an additional atypical "transitional" cell that contribute to pathological processes in IPF.  Individual IPF cells frequently co-expressed alveolar AT1, AT2, and conducting airway selective markers, demonstrating "indeterminate" states of differentiation not seen in normal lung development.  Pathway analysis predicted aberrant activation of canonical signaling via TGF-ß, HIPPO/YAP, P53, and AKT-PI3 Kinase.  Immunofluorescence confocal microscopy identified the disruption of alveolar structure and loss of the normal proximal-peripheral differentiation of pulmonary epithelial cells.  Single cell transcriptomic analyses of respiratory epithelial cells identified loss of normal epithelial cell identities and unique contributions of epithelial cells to the pathogenesis of IPF.  Present scRNA-seq transcriptomic analysis of normal and IPF respiratory epithelial cells provides a rich data source to further explore lung health and disease.

overall_design: Examination of expression profiling at single-cell level between IPF and Control.

first: Yan

last: Xu

first: Takako

last: Mizuno

first: Vincent

last: Funari

first: Barry

middle: R

last: Stripp

first: Jeffrey

last: Whitsett


title: RNA-dependent RNA polymerases-synthesized antisense ribosomal siRNAs silence pre-rRNA via the nuclear RNAi pathway in C. elegans

city: Hefei

first: Shouhong

last: Guang

state: Anhui

address: 443 HuangShan Road

department: School of Life Sciences

institute: University of Science & Technology of China

summary: The biogenesis of rRNA drives cell growth and proliferation, but mechanisms that modulate rRNA production remain poorly understood. We have conducted a genetic screen to look for factors that negatively regulate endo-siRNA generation in C. elegans, and identified the suppressor of siRNA (susi)-1and a new class of triphosphorylated antisense ribosomal siRNAs (risiRNAs). In susi-1 mutant, we observed an accumulation of siRNA sequences complementary to 18S and 26S rRNAs. risiRNAs are similar to 22G-RNA, as they are 22 nt in length and have a triphosphorylated guanidine at their 5'-end. The generation of risiRNAs depends on RNA-dependent RNA polymerases, but not the ERI/Dicer complex. risiRNAs act through the nuclear RNAi pathway and guide the Argonaute protein NRDE-3 to the nucleoli, which leads to a downregulation of pre-rRNA expression. Interestingly, low temperature and ultraviolet irradiation also induces the accumulation of risiRNA, suggesting potential regulatory functions. Cloned SUSI-1 shows homology to Dis3-like exonuclease 2 (Dis3L2) in other organisms, a gene identified as a key exonuclease involved in the 3' to 5' degradation of oligouridylated RNAs. We observed an accumulation of 3'-tail oligouridylated 26S rRNA in susi-1 mutant and in low temperature-treated animals. Consistently, the injection of 3'-tail oligouridylated 26S rRNA elicited a nuclear accumulation of NRDE-3. Our findings thus establish SUSI-1(ceDis3L2) as a suppressor of endo-siRNA generation, identify a novel class of risiRNAs that suppress pre-rRNA expression, and suggest a potential disease mechanism.

overall_design: In this study, we compared (1) the small RNAs from wild type N2 animals with susi-1(R457) mutant, (2) NRDE-3-associated small RNAs in wild type animals with in eri-1 animals, (3) small RNAs in animals grow at normal temperature 20oC and animals after a 4oC cold shock; (4) small RNAs in eri-1 animals with or without UV irradiation; (5) NRDE-3-associated small RNAs with or without UV irradiation. To understant the mechanism of risiRNA biogenesis, we further investigated the accumulation of oligouridylated 26S rRNA by (6) 26S rRNA tail-seq of wild type N2 with susi-1(ust1) animals; (7) 26S rRNA tail-seq of eri-1 animals with eri-1;susi1 animals; (8) 26S rRNA tail-seq of eri-1 animals with or without 4C cold shock.


title: DNase-seq from inferior parietal cortex (ENCSR986YWZ)


title: DNase-seq from A172 (ENCSR932KWJ)

summary:
DNase-seq on cell line A172 (53 year old male human brain, glioblastoma)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from PC-9 (ENCSR940NLN)

summary:
DNase-seq on PC-9 cell line (human lung adenocarcinoma)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from H9 (ENCSR943SYS)


title: DNase-seq from HeLa-S3 (ENCSR959ZXU)


title: genetic modification DNase-seq from K562 (ENCSR945ENZ)

summary:
TALEN-mediated homozygous DHS deletion in K562.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from hematopoietic multipotent progenitor cell (ENCSR937UWI)


title: genetic modification DNase-seq from K562 (ENCSR914PJE)


title: DNase-seq from spinal cord (ENCSR910OQF)

summary:
DNase-seq on 59 day fetal female human spinal cord

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from sigmoid colon (ENCSR907VOR)


title: genetic modification DNase-seq from K562 (ENCSR901BRM)


title: DNase-seq from thyroid gland (ENCSR902XFY)


title: DNase-seq from MN1 (ENCSR898KAX)


title: DNase-seq from embryonic facial prominence (ENCSR863XNX)


title: genetic modification DNase-seq from K562 (ENCSR873PLF)

summary:
TALEN-mediated heterozygous DHS deletion in K562.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from adrenal gland (ENCSR865ICK)


title: genetic modification DNase-seq from K562 (ENCSR997TXZ)


title: genetic modification DNase-seq from K562 (ENCSR982JMP)


title: DNase-seq from adrenal gland (ENCSR848XIY)


title: DNase-seq from hematopoietic multipotent progenitor cell (ENCSR845CFB)

summary:
DNase-seq on 25 year old human male hematopoietic multipotent progenitor cell

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from H9 (ENCSR964WHY)


title: genetic modification DNase-seq from K562 (ENCSR826CTO)


title: DNase-seq from SK-N-DZ (ENCSR946MVP)


title: DNase-seq from acute myeloid leukemia (ENCSR855ASN)


title: DNase-seq from ovary (ENCSR855DJV)


title: genetic modification DNase-seq from K562 (ENCSR967DXR)

summary:
TALEN-mediated heterozygous DHS deletion in K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from pons (ENCSR829MXU)


title: DNase-seq from trophoblast cell (ENCSR964MZQ)


title: DNase-seq from hematopoietic multipotent progenitor cell (ENCSR855FOP)


title: DNase-seq from HT-29 (ENCSR814KRX)

summary:
DNase-seq on immortalized cell line HT-29, epithelial cells from a 44 year old female adult human colon with a colorectal adenocarcinoma.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: genetic modification DNase-seq from K562 (ENCSR818YUC)


title: genetic modification DNase-seq from K562 (ENCSR815JAA)


title: DNase-seq from limb (ENCSR818JGZ)


title: DNase-seq from retina (ENCSR820ICX)


title: DNase-seq from occipital lobe (ENCSR859CZM)


title: DNase-seq from H4 (ENCSR809CEA)


title: DNase-seq from urinary bladder (ENCSR813CKU)

summary:
DNase-seq on 76 day old fetal male human urinary bladder tissue

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from glomerular visceral epithelial cell (ENCSR785BDQ)


title: DNase-seq from transverse colon (ENCSR790FIS)


title: DNase-seq from heart (ENCSR804RSI)


title: DNase-seq from right kidney (ENCSR768OLL)


title: DNase-seq from amniotic stem cell (ENCSR820WLP)


title: DNase-seq from H9 (ENCSR754LIN)


title: DNase-seq from heart (ENCSR749BWV)


title: DNase-seq from L1-S8R (ENCSR746ZPP)


title: genetic modification DNase-seq from K562 (ENCSR744QGM)


title: DNase-seq from midbrain (ENCSR706IDL)

summary:
DNase-seq on 78 year old male human adult midbrain tissue

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: genetic modification DNase-seq from K562 (ENCSR724SCF)


title: DNase-seq from MN1 (ENCSR732IZK)


title: DNase-seq from SJCRH30 (ENCSR700ILE)

summary:
DNase-seq of SJCHR30

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from heart (ENCSR705CNJ)


title: DNase-seq from trophoblast cell (ENCSR809LCE)


title: DNase-seq from ELF-1 (ENCSR678ILN)


title: DNase-seq from EL (ENCSR691MQJ)


title: DNase-seq from 3T3-L1 (ENCSR687EAW)

summary:
DNase-seq on 3T3-L1 mouse cell line (mouse embryo fibroblasts)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from Muller cell (ENCSR666HFH)

summary:
DNase-seq on mouse Muller cell

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from NAMALWA (ENCSR662HMO)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from heart (ENCSR664PKM)


title: genetic modification DNase-seq from K562 (ENCSR632CQZ)


title: genetic modification DNase-seq from K562 (ENCSR627GNV)


title: DNase-seq from eye (ENCSR782XFY)

summary:
DNase-seq on 76 day old fetal male human eye tissue

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: genetic modification DNase-seq from K562 (ENCSR636VCX)


title: DNase-seq from globus pallidus (ENCSR771DAX)

summary:
DNase-seq on 84 year old adult male human globus pallidal tissue

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from bipolar spindle neuron (ENCSR626RVD)


title: DNase-seq from tongue (ENCSR759UNY)

summary:
DNase-seq on 76 day old fetal female human tongue tissue

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from SJSA1 (ENCSR620WAR)

summary:
DNase-seq on immortalized cell line SJSA1 (fibroblast from 19 year old male human adult bone with osteosarcoma, multipotential sarcoma)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: genetic modification DNase-seq from K562 (ENCSR622RJN)


title: DNase-seq from HAP-1 (ENCSR620QNS)


title: genetic modification DNase-seq from K562 (ENCSR605SNG)


title: DNase-seq from brain (ENCSR595CSH)


title: DNase-seq from RPMI8226 (ENCSR594NOE)


title: DNase-seq from sigmoid colon (ENCSR592DQC)


title: DNase-seq from Ammon's horn (ENCSR584LUZ)


title: DNase-seq from lung (ENCSR582IPV)


title: DNase-seq from trophoblast cell (ENCSR593LTJ)


title: DNase-seq from esophagus squamous epithelium (ENCSR579BNV)


title: genetic modification DNase-seq from K562 (ENCSR577TXK)


title: DNase-seq from placenta (ENCSR575VMI)


title: DNase-seq from hematopoietic multipotent progenitor cell (ENCSR564JUY)

summary:
DNase-seq on 25 year old human adult male hematopoietic multipotent progenitor cell line

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from tongue (ENCSR559WMK)

summary:
DNase-seq on 72 day old male human fetal tongue tissue

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: genetic modification DNase-seq from K562 (ENCSR561XZU)


title: DNase-seq from limb (ENCSR532CRI)


title: genetic modification DNase-seq from K562 (ENCSR527IGO)

summary:
TALEN-mediated homozygous DHS deletion in K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from body of pancreas (ENCSR522WLH)


title: DNase-seq from heart left ventricle (ENCSR501FWC)


title: DNase-seq from EH (ENCSR548MMD)

summary:
DNase-seq on cell line BJ (foreskin fibroblasts from a newborn human male).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from putamen (ENCSR493VDS)


title: DNase-seq from placenta (ENCSR499IFY)


title: DNase-seq from Caki2 (ENCSR515EWI)

summary:
DNase-seq on cell line Caki-2 (epithelial cell from 69 year old male human kidney, clear cell carcinoma)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: genetic modification DNase-seq from K562 (ENCSR514EOB)

summary:
TALEN-mediated heterozygous DHS deletion in K562.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: genetic modification DNase-seq from K562 (ENCSR485CIR)

summary:
TALEN-mediated homozygous DHS deletion in K562.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from LoVo (ENCSR503BEM)


title: DNase-seq from umbilical cord (ENCSR512CWR)

summary:
DNase-seq on 76 day old male human fetal umbilical cord tissue

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from testis (ENCSR475SYH)


title: DNase-seq from hematopoietic multipotent progenitor cell (ENCSR493IAY)


title: DNase-seq from brain (ENCSR475VQD)

summary:
DNase-seq on 72 day old male human fetal brain tissue

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from MM.1S (ENCSR458LIB)


title: DNase-seq from prostate gland (ENCSR456SOX)


title: DNase-seq from embryonic facial prominence (ENCSR435NHO)


title: genetic modification DNase-seq from K562 (ENCSR560CCF)


title: genetic modification DNase-seq from K562 (ENCSR447ULX)


title: DNase-seq from hematopoietic multipotent progenitor cell (ENCSR420NOA)


title: DNase-seq from adipocyte (ENCSR405TXU)

summary:
DNase-seq on human adipocyte

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from MEL cell line (ENCSR446MUM)


title: DNase-seq from KBM-7 (ENCSR426IEA)

summary:
DNase-seq on cell line KBM-7 (human myeloid leukemia)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: genetic modification DNase-seq from K562 (ENCSR374YBC)


title: genetic modification DNase-seq from K562 (ENCSR518HJD)


title: DNase-seq from hepatocyte (ENCSR364MFN)

summary:
DNase-seq on 5 day embryonic female human IV-differentiated hepatocyte

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from CD1c-positive myeloid dendritic cell (ENCSR373BIX)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from superior temporal gyrus (ENCSR382JUJ)


title: DNase-seq from MEL cell line (ENCSR372SMH)


title: DNase-seq from hematopoietic multipotent progenitor cell (ENCSR362JSZ)


title: DNase-seq from A673 (ENCSR346JWH)

summary:
DNase-seq on cell line A673 (polygonal cell from 15 year old female human muscle, Ewing's sarcoma)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from Daoy (ENCSR346IHH)

summary:
DNase-seq on cell line Daoy (polygonal cell from 4 year old male human cerebellum, desmoplastic cerebellar medulloblastoma)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from middle frontal gyrus (ENCSR318PRQ)

summary:
DNase-seq on 78 year old male human middle frontal gyral tissue

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from HepG2 (ENCSR329MHM)

summary:
RNA-seq on human HepG2 (paired-ended)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: genetic modification DNase-seq from K562 (ENCSR274JIR)


title: DNase-seq from G401 (ENCSR269SIA)


title: DNase-seq from NCI-H226 (ENCSR265TEK)


title: DNase-seq from RKO (ENCSR429RHR)


title: DNase-seq from ACHN (ENCSR257BGZ)

summary:
DNase-seq on cell line ACHN (epithelial cell from 22 year old male human kidney, renal cell adenocarcinoma)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from ELR (ENCSR240TPI)


title: genetic modification DNase-seq from K562 (ENCSR423UEH)


title: DNase-seq from uterus (ENCSR237WJY)


title: DNase-seq from medulla oblongata (ENCSR224IYD)


title: genetic modification DNase-seq from K562 (ENCSR229PFU)


title: DNase-seq from SW480 (ENCSR217SET)


title: genetic modification DNase-seq from K562 (ENCSR215FCQ)


title: DNase-seq from adrenal gland (ENCSR191FOV)


title: DNase-seq from amniotic stem cell (ENCSR207TUX)


title: DNase-seq from right lobe of liver (ENCSR174TIP)


title: DNase-seq from gastrocnemius medialis (ENCSR171ETY)


title: DNase-seq from HepG2 (ENCSR149XIL)


title: genetic modification DNase-seq from K562 (ENCSR165BGV)


title: DNase-seq from left kidney (ENCSR097BWW)

summary:
DNase-seq on 91 day old male fetal human kidney tissue

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from trophoblast cell (ENCSR121ZSL)


title: genetic modification DNase-seq from K562 (ENCSR064EFK)


title: DNase-seq from thyroid gland (ENCSR158VAT)


title: genetic modification DNase-seq from K562 (ENCSR048BUO)


title: genetic modification DNase-seq from K562 (ENCSR154AVE)


title: DNase-seq from L1-S8 (ENCSR314EZY)


title: genetic modification DNase-seq from K562 (ENCSR101TGA)


title: DNase-seq from hematopoietic multipotent progenitor cell (ENCSR098PTC)


title: DNase-seq from RCC 7860 (ENCSR037PGI)

summary:
DNase-seq of RCC 7860 (human renal carcinoma cell, 58 year old male)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from hematopoietic multipotent progenitor cell (ENCSR148VUP)

summary:
DNase-seq on 25 year old human adult male hematopoietic multipotent progenitor cell line

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from PC-3 (ENCSR052AWE)


title: total RNA-seq from MEL cell line (ENCSR000CWF)

summary:
RNA-seq on mouse MEL treated by dimethyl sulfoxide at 2.0%

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: genetic modification DNase-seq from K562 (ENCSR141VJJ)


title: total RNA-seq from MEL cell line (ENCSR000CWE)

summary:
Stanford mouse MEL RNA-seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from stomach (ENCSR095GWE)


title: total RNA-seq from mononuclear cell (ENCSR000CUT)

summary:
The libraries contained in this experiment come from mononuclear peripheral blood primary whole cells, hMNC-PB isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from body of pancreas (ENCSR228IKB)


title: DNase-seq from kidney (ENCSR066WZJ)


title: genetic modification DNase-seq from K562 (ENCSR087QUG)

summary:
TALEN-mediated heterozygous DHS deletion in K562.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from MG63 (ENCSR083STA)

summary:
DNase-seq on 14 year old male human MG63 immortalized cell line

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from induced pluripotent stem cell (ENCSR004SUL)


title: genetic modification DNase-seq from K562 (ENCSR137EEM)

summary:
TALEN-mediated heterozygous DHS deletion in K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: genetic modification DNase-seq from K562 (ENCSR167DFU)

summary:
TALEN-mediated homozygous DHS deletion in K562.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from eye (ENCSR127PWK)

summary:
DNase-seq on 76 day old female human eye tissue

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from caudate nucleus (ENCSR015BGH)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from ES-E14 (ENCSR000CWC)

summary:
Stanford mouse ES-E14 RNA-seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from SJCRH30 (ENCSR000FFJ)

summary:
SJCRH30 DNase-seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GM12878 (ENCSR000CVT)

summary:
The libraries contained in this experiment come from the nucleolar fraction of independent growths of cell line GM12878. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from CD14-positive monocyte (ENCSR000CUC)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent isolates of mobilized CD14+ monocytes. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from H9 (ENCSR017OZH)


title: polyA mRNA RNA-seq from SK-N-SH (ENCSR000CTR)

summary:
The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line SK-N-SH. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from IMR-90 (ENCSR000CTQ)

summary:
RNA-seq on human IMR90 whole cell long polyA+ RNA

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from mesenchymal stem cell of adipose (ENCSR000CTZ)

summary:
The libraries contained in this experiment come from mesenchymal adipose derived stem cells, hMSC-AT isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from mesenchymal stem cell of the bone marrow (ENCSR000CUD)

summary:
The libraries contained in this experiment come from mesenchymal bone marrow derived stem cells, hMSC-BM isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from MCF-7 (ENCSR000CTU)

summary:
The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line MCF-7. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from CD14-positive monocyte (ENCSR000CTY)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent isolates of mobilized CD14+ monocytes. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from B cell (ENCSR000CTV)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent isolates of CD20+ B cells. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from SK-N-SH (ENCSR000CTS)

summary:
The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line SK-N-SH. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from SK-N-SH (ENCSR000CTT)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line SK-N-SH. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from MCF-7 (ENCSR000CTO)

summary:
The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line MCF-7. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from IMR-90 (ENCSR000CTK)

summary:
RNA-seq on human IMR90 whole cell long total RNA

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from mesenchymal stem cell of Wharton's jelly (ENCSR000CUO)

summary:
The libraries contained in this experiment come from mesenchymal umbilical cord derived stem cells, hMSC-UC isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from A549 (ENCSR000CTL)

summary:
The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line A549. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from A549 (ENCSR000CTM)

summary:
The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line A549. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from H1-hESC (ENCSR000CQR)

summary:
The libraries contained in this experiment come from the nuclear fraction of independent growths of the human embryonic stem cell line H1-hESC. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from HepG2 (ENCSR000CQU)

summary:
The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from endothelial cell of umbilical vein (ENCSR000CQS)

summary:
RNA-seq on human HUVEC cytosol long polyA- RNA

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from H1-hESC (ENCSR000CQQ)

summary:
The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of the human embryonic stem cell line H1-hESC. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized  Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from HeLa-S3 (ENCSR000CQT)

summary:
The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from B cell (ENCSR000CTW)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent isolates of CD20+ B cells. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from HeLa-S3 (ENCSR000CQJ)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from K562 (ENCSR000CQL)

summary:
The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line K562. They are stranded PE76 Illumina GaIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from K562 (ENCSR000CQM)

summary:
The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from IMR-90 (ENCSR000CTN)

summary:
RNA-seq on human IMR90 cytosol long polyA+ RNA

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from GM12878 (ENCSR000CQF)

summary:
The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line GM12878. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from SK-N-SH (ENCSR000CQP)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line SK-N-SH that has been treated with retinoic acid. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from IMR-90 (ENCSR000CTP)

summary:
The libraries contained in this experiment come from lung fibroblasts primary nuclear extracts, IMR90. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from HepG2 (ENCSR000CQK)

summary:
The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from HeLa-S3 (ENCSR000CQI)

summary:
The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from foreskin fibroblast (ENCSR000CQD)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of foreskin fibroblast cells. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from A549 (ENCSR000CQC)

summary:
The libraries contained in this experiment come from whole cell fractions of independent growths of cell line A549. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from MCF-7 (ENCSR000CQB)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line MCF-7. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from K562 (ENCSR000CPZ)

summary:
The libraries contained in this experiment come from the nucleolar fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from GM12878 (ENCSR000CQE)

summary:
The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line GM12878. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from K562 (ENCSR000CQA)

summary:
The libraries contained in this experiment come from the nucleoplasm fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from K562 (ENCSR000CPY)

summary:
The libraries contained in this experiment come from the chromatin fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from GM12878 (ENCSR000CPO)

summary:
The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line GM12878. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from MCF-7 (ENCSR000CPT)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line MCF-7. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from HeLa-S3 (ENCSR000CPQ)

summary:
The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from HepG2 (ENCSR000CPD)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from K562 (ENCSR000CPG)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from HepG2 (ENCSR000CPF)

summary:
The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from SK-N-SH (ENCSR000CPN)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line SK-N-SH that has been treated with retinoic acid. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from HeLa-S3 (ENCSR000CPP)

summary:
The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from H1-hESC (ENCSR000COT)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of the human embryonic stem cell line H1-hESC. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized  Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA depleted RNA-seq from GM12878 (ENCSR000COS)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line GM12878. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from foreskin fibroblast (ENCSR000COP)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of foreskin fibroblast cells. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from H1-hESC (ENCSR000COW)

summary:
The libraries contained in this experiment come from the nuclear fraction of independent growths of the human embryonic stem cell line H1-hESC. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from GM12878 (ENCSR000COR)

summary:
The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line GM12878. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from H1-hESC (ENCSR000COU)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of the human embryonic stem cell line H1-hESC. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from H1-hESC (ENCSR000COV)

summary:
The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of the human embryonic stem cell line H1-hESC. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from K562 (ENCSR000COK)

summary:
The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from megakaryocyte-erythroid progenitor cell (ENCSR000CIF)

summary:
RNA-seq on mouse megakaryocyte-erythroid progenitor cells (paired end)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from G1E-ER4 (ENCSR000CHX)

summary:
RNA-seq on mouse G1E-ER4 (paired end) differentiated for 7 hours

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from G1E-ER4 (ENCSR000CHY)

summary:
RNA-seq on mouse G1E-ER4 (paired end)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from megakaryocyte (ENCSR000CIC)

summary:
RNA-seq on mouse megakaryote (paired end)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from G1E-ER4 (ENCSR000CHZ)

summary:
RNA-seq on mouse G1E-ER4 (paired end) differentiated for 3 hours

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from G1E-ER4 (ENCSR000CHW)

summary:
RNA-seq on mouse G1E-ER4 (paired end) differentiated for 14 hours

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from G1E-ER4 (ENCSR000CIA)

summary:
RNA-seq on mouse G1E-ER4 (paired end) differentiated for 24 hours

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from K562 (ENCSR000CPS)

summary:
The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from G1E-ER4 (ENCSR000CIB)

summary:
RNA-seq on mouse G1E-ER4 (paired end) differentiated for 30 hours

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from leukemia stem cell (ENCSR000CHT)

summary:
RNA-seq on mouse FVL stem (paired end)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from G1E (ENCSR000CHV)

summary:
RNA-seq on mouse G1E (paired end)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from HepG2 (ENCSR000CPC)

summary:
The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from erythroblast (ENCSR000CHS)

summary:
RNA-seq on mouse erythroblast (paired end)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from hematopoietic multipotent progenitor cell (ENCSR000CHU)

summary:
RNA-seq on mouse FV progenitor (paired end)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from G1E (ENCSR000CIG)

summary:
RNA-seq on mouse G1E (single end)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from cortical plate (ENCSR000BZR)

summary:
The libraries contained in this experiment come from adult 8 week cortical brain tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from frontal cortex (ENCSR000BZS)

summary:
The libraries contained in this experiment come from adult 8 week frontal cortex tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from urinary bladder (ENCSR000BZQ)

summary:
The libraries contained in this experiment come from adult 8 week bladder tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from placenta (ENCSR000BZP)

summary:
The libraries contained in this experiment come from adult 8 week placental tissue from staged pregnant females in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from limb (ENCSR000BZN)

summary:
The libraries contained in this experiment come from embryonic day 14.5 (E.14.5) limb tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from central nervous system (ENCSR000BZK)

summary:
The libraries contained in this experiment come from embryonic day 14 (E.14) central nervous system tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from central nervous system (ENCSR000BZL)

summary:
The libraries contained in this experiment come from  embryonic day 18 (E.18) central nervous system tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from brain (ENCSR000BZJ)

summary:
The libraries contained in this experiment come from embryonic day 14.5 (E.14.5) whole brain tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from subcutaneous adipose tissue (ENCSR000BZF)

summary:
The libraries contained in this experiment come from adult 8 week subcutaneous fat pad tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from liver (ENCSR000BZI)

summary:
The libraries contained in this experiment come from embryonic day 14.5 (E.14.5) liver tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from central nervous system (ENCSR000BZG)

summary:
The libraries contained in this experiment come from embryonic day 11.5 (E11.5) central nervous system tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from stomach (ENCSR000BZE)

summary:
The libraries contained in this experiment come from adult 8 week stomach tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from liver (ENCSR000BZH)

summary:
The libraries contained in this experiment come from embryonic day 14 (E.14) liver tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from cerebellum (ENCSR000BZM)

summary:
The libraries contained in this experiment come from adult 8 week cerebellum tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from duodenum (ENCSR000BYY)

summary:
The libraries contained in this experiment come from adult 8 week duodenum tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from gonadal fat pad (ENCSR000BYZ)

summary:
The libraries contained in this experiment come from adult 8 week genital fat pad tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from mammary gland (ENCSR000BZB)

summary:
The libraries contained in this experiment come from adult 8 week mammary gland tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from thymus (ENCSR000BYV)

summary:
The libraries contained in this experiment come from adult 8 week thymus tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from large intestine (ENCSR000BZA)

summary:
The libraries contained in this experiment come from adult 8 week large intestine tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from small intestine (ENCSR000BZD)

summary:
The libraries contained in this experiment come from adult 8 week small intestine tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from ovary (ENCSR000BZC)

summary:
The libraries contained in this experiment come from adult 8 week ovaries tissue from female littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from liver (ENCSR000BYS)

summary:
The libraries contained in this experiment come from adult 8 week liver tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from kidney (ENCSR000BYR)

summary:
The libraries contained in this experiment come from adult 8 week kidney tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from testis (ENCSR000BYW)

summary:
The libraries contained in this experiment come from adult 8 week testes tissue from male littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from liver (ENCSR000BZO)

summary:
The libraries contained in this experiment come from embryonic day 18 (E.18) liver tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from spleen (ENCSR000BYU)

summary:
The libraries contained in this experiment come from adult 8 week spleen tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from heart (ENCSR000BYQ)

summary:
The libraries contained in this experiment come from adult 8 week heart tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from lung (ENCSR000BYT)

summary:
The libraries contained in this experiment come from adult 8 week lung tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from myocyte (ENCSR000AIA)

summary:
RNA-seq on mouse C2C12 differentiated for 60 hours polyA+

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from adrenal gland (ENCSR000BYX)

summary:
The libraries contained in this experiment come from adult 8 week adrenal gland tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from colon (ENCSR000BYP)

summary:
The libraries contained in this experiment come from adult 8 week colon tissue from mixed sex littermates in mouse strain C57BL/6J. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from U-87 MG (ENCSR000BYO)

summary:
RNA-seq on U87 greater than 200bp polyA+

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from C2C12 (ENCSR000AHY)

summary:
RNA-seq of C2C12 polyadenlated RNA

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from C3H10T1/2 (ENCSR000AHZ)

summary:
RNA-seq of 10T1-2 polyadenlated RNA

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from C3H10T1/2 (ENCSR000AHX)

summary:
RNA-seq on mouse 10T1-2 treated with differentiation treatment (control) for 60 hours polyA+

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Activation of Notch1 synergizes with multiple pathways in promoting castration-resistant prostate cancer

city: Palo Alto

first: Tanya

last: Stoyanova

state: California

address: 3155 Porter Drive, Palo Alto, CA 94304

department: Radiology

institute: Stanford University

summary: Chronic activation of Notch1 synergizes with multiple oncogenic pathways altered in early prostate cancer to promote the development of prostate adenocarcinoma. Expression profiling revealed that these tumors display features of epithelial-to-mesenchymal transition, a cellular state associated with increased tumor aggressiveness.Tumors driven by Notch1 intracellular domain in combination with multiple pathways altered in prostate cancer are metastatic and resistant to androgen deprivation.

overall_design: Mouse prostate tumors initiated by the combination of NICD1/kRasG12D, NICD1/myrAKT, or NICD/Myc and normal mouse prostates were subjected to high-throughput RNA-sequencing and differential gene-expression analysis


title: m6A controls neurogenesis and sex determination in Drosophila via its nuclear reader protein YT521-B [RNA-Seq, whole flies]

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

summary: N6-methyladenosine RNA (m6A) is the most abundant internal mRNA modification in mammals. While its role in the regulation of posttranscriptional gene expression is beginning to be unveiled, its function during development of complex organisms is poorly understood. Here, we identify Spenito as a novel member of the methyltransferase complex and show that m6A in Drosophila is necessary for proper synaptic growth, and in regulation of early steps of pre-mRNA splicing. Splicing of Sex-lethal and of its downstream targets are defective in animals lacking m6A, revealing also important roles in sex determination and dosage compensation. Finally, we implicate the nuclear m6A reader protein, YT521-B, as a crucial effector of m6A modifications in vivo. Altogether, our work provides important novel insights into m6A biology through identification and characterization of both m6A-writing and -reading proteins in Drosophila and their effects on splicing, neurogenesis and sex-determination within the context of the whole animal.

overall_design: RNA seq in Drosophila melanogaster (flies) (3 Conditions, triplicates)

first: Tina

last: Lence

first: Junaid

last: Akhtar

first: Marc

last: Bayer

first: Katharina

last: Schmid

first: Laura

last: Spindler

first: Cheuk

last: Ho

first: Nastasja

last: Kreim

first: Miguel

last: Andrade-Navarro

first: Burkhard

last: Poeck

first: Mark

last: Helm