title: In-vivo inhibition of Fgfr2b signalling in embryonic whole mouse lungs at E16.5

summary: In this experiment we inhibited FGF signalling in E16.5 mouse lungs by using a dominant negative mouse model. We are interested in assessing the genetic regulation by FGF signalling at this stage of lung development.  Specifically, we used a tetracycline controlled transcriptional activation model (Tet(o)) to manipulate FGF signalling. Genetically modified male mice that expressed a reverse tetracycline-controlled trans activator (rtTA) on the Rosa26 locus and a soluble FGFR2b on the Tet(o) promoter (Tet(o)sFgfr2b) (B6.Cg-Gt(ROSA)26Sortm1.1(rtTA,EGFP)NagyTg(tetO-Fgfr2b/Igh)1.3Jaw/sbel), were crossed with females lacking the Tet(o)sFgfr2b allele. Pregnant females were injected with doxycycline intraperitonally at E16.5. Doxycycline then induced the transcription soluble FGFR2b in the embryos, which inhibited FGF signalling by sequestering FGF ligands, preventing them from binding to the native FGFR2b receptor. We harvested embryonic lungs after 9 hrs of inhibition. We took the left lobe of each sample for RNA isolation. We set-up our matings so that 50% of the embryos in a litter were expected to contain the soluble FGFR2b. The remaining littermates will serve as the control group. We will compare the gene expression profiles of the experimental embryonic lungs with those of littermate controls.

overall_design: 2 groups, each with 3 to 5 biological replicates


title: Impact of hydrogen peroxide (H2O2) on transcription in Jurkat T cells

status: Public on Jun 01 2021

city: Paris cedex 15

first: Christian

last: MUCHARDT

address: 25 rue du Dr-Roux

department: Developmental and Stem Cell Biology

country: France

institute: Institut Pasteur Paris

type: Expression profiling by high throughput sequencing

summary: Accumulation of senescent cells is an important contributor to chronic inflammation upon aging. While the transcription factors driving the inflammatory phenotype of senescent cells have been extensively studies, the triggers of the pro-inflammatory pathways are still incompletely characterized. Here, we show that cells driven into senescence by different routes share a deficiency in RNA degradation activity most correlated with reduced expression of one or several subunits of the RNA exosome. A similar deficiency was also detected in cells exposed to oxidative stress, either acute, by treatment with hydrogen peroxide, or more long-term in a mouse model for mitochondrial suffering. Reciprocally, inactivation of RNA exosome activity reduced expression of mitochondrial genes while promoting senescence markers, suggesting that the RNAs accumulating as a consequence of the reduced turnover, have a function in promoting some aspects of the senescent phenotype. Consistent with this, we show that some of the RNA species detected in senescent cells are also produced during normal activation of immune cells and contain Alu sequences known to trigger an innate immune response. We propose that these RNA species participate in driving and maintaining the permanent inflammatory state characteristic of cellular senescence.

overall_design:
Jurkat cells were exposed to either H2O, or 2mM H2O2 for 30 min. Total RNAs were isolated with a phenol-chloroform-based protocole. Stranded libraries were prepared by random priming, enrichched in poly(A),
and then sequenced with a paired end protocole.

first: Saliha

last: AZEBI

first: Mickaël

last: COSTALLAT


title: Tissues' transcriptome sequence of Silurus meridionalis

city: Shenzhen

first: Fan

middle: ding

last: ding

address: yantian shashen Road

country: China

institute: EasyATCG

summary: 18 tissues' transcriptome sequence of Silurus meridionalis

overall_design:
RNA-seq of multiple tissues from adult fish.
Raw files are available at: PRJNA427243,SRP148534

first: Yaoguang

last: Zhang

first: Deshou

last: Wang

first: Zuogang

last: Peng


title: Tissues' transcriptome sequence of Silurus asotus

summary: 15 tissues' transcriptome sequence of Silurus asotus

overall_design:
RNA-seq of multiple tissues from adult fish.
Raw files are available at: PRJNA427250,SRP146370


title: Chromatin and transcriptome remodeling under EGFR chemical inhibition in lung cancer

city: New York

first: Eric

middle: Edison

last: Gardner

state: New York

address: 413 East 69th Street, BRB-1352

department: Medicine

country: USA

institute: Weill Cornell Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Identification of the transcription factor FOXL2 as a negative regulator of ovarian cancer progression.

city: Jerusalem

first: Rotem

last: Karni

address: Hadassah Ein-Kerem

country: Israel

institute: Hebrew University of Jerusalem


title: MicroRNA expression profile in splenic B cells of C57BL/6 mice in the late phase of Schistosoma japonicum infection

city: Yangzhou

first: fang

last: tian

state: Jiangsu

address: huai hai road 11

department: Institute of Translational Medicine

institute: Yangzhou university

summary: Background: Schistosomiasis remains an important global public health problem that affects 285 million people in 78 countries. The immune response mechanisms of host–parasite interaction are complex, and miRNAs play a major role in modulation of development, homeostasis, as well as the function of immune cells. Results: In this study, an miRNA microarray was applied to investigate differences in miRNA expression in splenic B cells of normal and 13w post infected mice. In total, 43 miRNAs were detected in splenic B cells of the C57BL/6 mice before and after infection, including 33 miRNAs with up-regulated expression, and 10 miRNAs with down-regulated expression in mice 13w infection with schistosomes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the differentially expressed miRNAs revealed that many important biological pathways are triggered by schistosome infection in C57BL/6 mice, such as the Thyroid hormone signal pathway, Axon guidance, insulin signaling pathway, Pathways in cancer and Rap1 signaling pathway. The results reveal that miRNAs may be an important regulator of splenic B cells in the chronic phase of Schistosoma japonicum infection. Conclusions: The data presented here provide valuable information to increase understanding of the basic role of miRNAs in splenic B cells during the interaction of the S. japonicum with the host. This may be helpful in identifying the upstream molecular pathways controlling B cell specialization and provides a new platform of B cell manipulation to fine-tune their function.

overall_design: In this study, an miRNA microarray was applied to investigate differences in miRNA expression in splenic B cells of uninfected and 13w post infected mice with schistosoma japonicum. There were 3 samples in the infected group and 3 samples in the uninfected group as control.Three independent experiments were performed using different mouse for each experiment.

first: Fang

last: Tian

first: Bin

last: Yang

first: Mengqi

last: Xu

first: Ziwen

first: Tiantian

first: Li

last: Qian

first: Weiping


title: Identification of changes in gene expression after knock down of FOXL2 in patient derived immortal fallopian tube cells [CEL-Seq]

summary: In order to identify specific events that are causatively involved in the metastatic process, we analyzed matched samples from 3 high grade serous ovarian cancer patients by RNA-seq. For each patient we examined samples representing the three cancer states: 1) primary tumor; 2) omentum metastasis (solid metastasis); 3) effusion metastasis. We identified genes differentially expressed between the various states. One of the genes found to be expressed in the primary tumor but not in the omentum or effusion metastasis is FOXL2, a transcription factor known to play a role in ovarian development and function. This change was successfully validated by RT-PCR in both the patients' samples as well as in a set of 27 independent patient samples representing the three cancer states. Knock-down of FOXL2 in patient-derived immortal fallopian tube cells lead to increased proliferation and survival. RNA-seq of the immortal fallopian tube cells after FOXL2 knock-down revealed a pro-metastatic gene expression signature. Our results suggest that FOXL2 is an important tumor suppressor and an inhibitor of ovarian cancer progression.

overall_design: mRNA profiling of 2 patient derived immortal fallopian tube cells with and without FOXL2 siRNA by CEL-seq analysis

first: Adi

last: Mogilevsky

first: Ilana

middle: L

last: Loinger

first: Zahava

last: Siegfried

first: Keren

middle: B

last: Shany

first: Reuven

last: Reich

first: Eitan

last: Winter

first: Hadar

last: Benyamini

first: Sharona

last: Elgavish

first: Marc

last: Sultan

first: Marie

last: Yaspo

last: Levanon

first: Ben

last: Davidson


title: The effect of STARD3 knockdown  on melanoma cell line MeWo

city: Fukuoka

first: Yuhui

last: Huang

address: Hakozaki 6-10-1

department: Department of Bioscience and Biotechnology

country: Japan

institute: Faculty of Agriculture, Kyushu University

summary: Little is known about the role of  STARD3 in melanoma. We performed microarrays to revealed the transcriptional change of a human melanoma cell line (MeWo) to scr-shRNA and STARD3-shRNA  in order to provide insight into the role of STARD3 in MeWo cells.

overall_design: MeWo cells were stably transfected with scr-shRNA and STARD3-shRNA and total RNA was extracted by using TRIzol Reagent. Affymetrix Microarray analysis was conducted on the MeWo cells expressing by using Affymetrix Microarray chip.

first: Hirofumi

last: Tachibana


status: Public on May 31 2021

city: Madison

first: Andy

last: Madrid

state: Wisconsin

address: 600 Highland Ave

department: Neurological Surgery

institute: University of Wiconsin - Madison

summary: Genome-wide DNA methylation analysis of COVID-19 severity using the Illumina HumanMethylationEPIC microarray platform to analyze over 850,000 methylation sites, comparing COVID-19 patients with patients presenting with respiratory symptoms, but negative for COVID-19, using whole blood tissue.

overall_design: Bisulfite converted DNA from whole blood tissue from 102 COVID-19 patients compared to 26 non-COVID-19 patients were run on the Illumina HumanMethylationEPIC platform.

first: Reid

middle: S

last: Alisch


title: In-vivo inhibition of Fgfr2b signalling in FACS-isolated Sftpc-expressing cells in embryonic mouse lungs from E14.5 to E18.5

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

summary: We are interested in studying the role of FGF/FGFR2b signalling on lung alveolar epithelial bipotent progenitors. Bipotent progenitors give rise to alveolar type 1 and type 2 cells (AECI and AECII, respectively). Previous research has shown that AECII cells isolated from lungs where FGF signalling has been globally inhibited  show a gene signature much closer to type 1 cells. Furthermore, the relative number of AECI in experimental lungs was increased compared to control lungs. This suggests FGF signalling promotes AECII differentiation. We want to test the hypothesis that FGF signalling promotes the differentiation of AECII by signalling to bipotent progenitors. To test this hypothesis, we have used a transgenic mouse line (SpcCreERT2_Fgfr2bflox_tomatoflox), which, upon administration of tamoxifen, can be used to knock-out the FGFR2b receptor in SFTPC + cells, while labelling those cells red. We injected mice carrying embryos with and without the Fgfr2bflox allele (experimental and control, respectively) at E14.5 and at E15.5. At this timepoint, SFTPC is a marker for bipotent progenitors. Thus, by administering tamoxifen at this timepoint, bipotent progenitors were targeted to knock-out FGFR2b, and thus inhibit FGF/FGFR2b signalling to these cells. We harvested lungs at E18.5, a timepoint where the differentiation of AECI and AECII is well underway. Harvested lungs were prepared for FACS-based cell sorting. Cells were sorted by gating for total epithelial cells, then RFP + cells (representing bipotent progenitors), then AECI and AECII cells. These cells were collected, and their total RNA isolated for gene array analysis. We will then compare the AECI and AECII gene signatures of isolated cells between experimental and control samples.

overall_design: 4 groups, each with 2 biological replicates

first: Cho-Ming

last: Chao


title: Role of RUVBL2 in LPS-induced proinflammatory gene expression of RAW264.7 cells

city: Hong Kong

first: Kwong Wai

last: CHOY

address: Hong Kong

department: O and G

country: Hong Kong

institute: CUHK

summary: The aim of this experiment is to compare gene expression proflies of RAW264.7 cells trasnfected with non-targeting siRNA or siRNA against RUVBL2, in the presence or absence of LPS.

overall_design: RNAs were obtained from cells transfected with non-targeting siRNA or siRNA against RUVBL2, subjected to cDNA synthesis and labeling, followed by hybridization to DNA microarray chips


title: MeRIP-seq analysis of transcript profiles during human umbilical cord mesenchymal stem cells osteogenic differentiation

city: Chengdu

first: Wenchuan

last: Chen

state: Sichuan

address: renmin sothroad

institute: Sichuan university

type: Methylation profiling by high throughput sequencing

summary: To assess the m6A methylome during osteogenic differentiation process of human umbilical cord mesenchymal stem cells, the methylated RNA immunoprecipitation sequencing (MeRIP-seq) was performed.

overall_design: Altered m6A-tagged transcript profiles in human umbilical cord mesenchymal stem cells  were measured at 7 days after osteogenic differentiation

first: Cheng

last: Su

first: Yanjin

last: He

first: Xiao

last: Zheng


title: Comparative Transcriptomic and Molecular Pathway Analyses of HL-CZ Human Pro-Monocytic Cells Expressing SARS-CoV-2 Spike S1, S2, NP, NSP15 and NSP16 Genes

city: Singapore

first: Vincent

last: Chow

address: 5 Science Drive 2, Blk MD4, Level 3

department: Microbiology & Immunology

country: Singapore

institute: National University of Singapore

summary: In order to better understand the biological roles of critical SARS-CoV-2 proteins, we determined and compared the host transcriptomic responses of the HL-CZ human promonocytic cell line upon transfection with key viral genes encoding the spike S1 subunit, S2 subunit, nucleocapsid (NP) protein, NSP15 (endoribonuclease), and NSP16 (2′-O-ribose-methyltransferase).

overall_design: mRNA profiles of HL-CZ cells transfected with pCMV3 and pCMV3-C-FLAG as control vs.  pCMV3-S1, pCMV3-S2, pCMV3-NP-FLAG, pCMV3-EN (NSP15), and pCMV3-ME (NSP16)

first: Anshika

last: Sharma

first: Joe

middle: W

last: Ong

first: Mun

middle: F

last: Loke

first: Eng

middle: G

last: Chua

first: Joseph

middle: J

last: Lee

first: Hyung

last: Choi

first: Yee

last: Tan

first: Sunil

middle: K

last: Lal

middle: T


title: Hepatic p53 protein level governs liver s sensitivity to drug-induced liver injury

city: Boston

first: Zhi-Min

last: Yuan

state: Massachusetts

address: 677 Huntington Ave.

department: Environmental Sciences

institute: Harvard University


title: Microarray of MDMX C462A and wildtype mice treated with acetaminophen

summary: We report the application of microarray sequencing technology for profiling of acetaminophen response in MDMXC462A mice. These data were used to evaluate differential gene expression and changes in cell composition using canonical markers for mouse liver cells.

overall_design: Examination of differential transcriptional response when wildtype and mdmx c462A/wt MEFs were treated with PMA, DMSO, JBL5, or no treatment.

first: Cb

last: Lim

first: Jiawei

last: Yan

first: Lizhen

last: Li

first: Monika

last: Lewinska

first: Cody

last: Rasmussen-Ivey

first: Jing

last: Jin


title: Differential transcriptional networks in malaria - the BioInflame study

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps University Marburg

summary:
PBMCs were isolated from patients suffering from Malaria or from healthy donors. RNA was extracted from these samples.
400 ng RNA per sample were then reverse transcribed with the Life Technologies miR RT kit with megaplex primers. Reverse transcribed RNA was then loaded on the human Taqman Low Density Array (TLDA) Cards and run according to manufacturer´s recommendations

overall_design: microRNA profiles were used to in silico build a biomarker network to discrimintate Malaria from healthy donors


title: Expression analysis of A375 melanoma cells with silenced BMI-1 or not

city: Xi’an

first: Yanting

last: Liu

address: 157 Xiwu Road

department: Dermatology

institute: Northwest Hospital, Xi’an Jiaotong University

summary: Our studies demonstrate that BMI-1 plays a crucial role in the EMT process and drug resistance in melanoma. Silencing Bmi-1 significantly inhibites the aggressive behavior and improves the chemosensitivity to all-trans retinoic acid on melanoma cells. We compared the different genes expression of A375-vector and A375-BMI-1 cells for exploring the underlying mechanisms of BMI-1 regulation on melanoma.

overall_design: A two chip study using total RNA recovered from two cultured cells, A375-vector and A375-BMI-1, which were transfected with empty lentivirus and target sequences shBMI-1. Silenced BMI-1 in A375-shBMI-1 cells was confirmed by real-time PCR and western blot analysis comparing to the control cells.

first: Songmei

last: Geng


title: ChIP-Seq analysis of PPARγ binding sites in iNKT cells

city: Hefei

first: Sicheng

last: Fu

address: Huangshan road

institute: USTC

summary: Chromatin immunoprecipitation-Sequence (ChIP-Seq) analysis indicated increased binding of PPARγ to Srebf1 promoter region after activating iNKT cells, and that was inhibited by T007—PPARγ inhibitor .


title: Physiological and transcriptomic analyses reveal sulfur is essential for cadmium detoxification and accumulation in poplar leaves

city: Beijing

first: Hong

middle: Yu

last: Zhang

address: Qinglongqiao Street

department: Research Institute of Forestry

institute: Chinese Academy of Forestry

type: Non-coding RNA profiling by high throughput sequencing

summary: Although poplars are good candidates for the phytoremediation of cadmium (Cd)-polluted soils and sulfur is a key player in modulating Cd detoxification and accumulation in plants, the physiological and molecular mechanisms underlying sulfur-mediated Cd accumulation remain largely unknown. To investigate physiological and transcriptomic regulation mechanisms of poplars in response to Cd exposure and different sulphate (S) supply levels, Populus deltoides saplings were exposed to either 0 or 50 µM Cd together with one of low, moderate and high S levels. Cd was accumulated in the leaves of Cd-exposed poplars under moderate S condition, and its accumulation is inhibited by low S but tended to increase by high S. Sulfur nutrition became deficient in Cd-treated leaves, and it was aggravated by low S but improved by high S. Concentrations of cysteine and glutathione were increased in Cd-treated leaves, and the Cd-induced increases were limited by low S but stimulated by high S. In line with the physiological changes, a number of mRNAs and microRNAs (miRNAs) involved in Cd accumulation and sulfur assimilation were identified and the miRNAs-mRNAs networks were dissected. In the networks, miR395 and miR399 members were identified as hub miRNAs and their targets were ATP sulfurylase 3 (ATPS3), and phosphate 2 (PHO2) and beta galactosidase 1 (BGAL1), respectively. These results suggest that Cd-induced changes in Cd accumulation and sulfur assimilation are exacerbated by low S but alleviated by high S supply, and that miRNAs-mRNAs regulatory networks play pivotal roles in sulfur-mediated Cd detoxification and accumulation in poplars.

overall_design: Each group of the six plants supplied with (0 (low, L), 100 (middle, M), and 1500 (high, H) µM) for 12 days. Afterwards, the plants in each group were further divided equally into two subgroups and exposed to either 0 (-Cd) or 50 (+Cd) μM CdCl2 together with the S treatments for 21 additional days.

first: Wenguang

last: Shi

first: Wenzhe

first: Chaofeng

last: Ma

first: Yuhong

first: Shen

last: Ding

first: Wenjian

last: Yu

first: Shurong

last: Deng

last: Zhou

first: Zhi-Bin

last: Luo


title: Identification of changes in gene expression between cancer states taken from high grade serous ovarian cancer patients [RNA-Seq]

first: Rotem

last: Karni

overall_design: mRNA profiling of 9 human serous ovarian cancer samples from 3 different patients by Illumina technology.

first: Adi

last: Mogilevsky

first: Ilana

last: Loinger

first: Zahava

last: Siegfried

first: Keren

last: Shany

first: Reuven

last: Reich

first: Eitan

last: Winter

first: Hadar

last: Benyamini

first: Sharona

last: Elgavish

first: Marc

last: Sultan

first: Marie

last: Yaspo

last: Levanon

first: Ben

last: Davidson


title: Effect of Cell Division on Cell Differentiation (RNA-Seq H9 cells UD E24 E24HU E24Noc)

city: Cambridge

first: Rodrigo

middle: Andres

last: Grandy

address: Cambridge Stem Cell Institute/ Anne McLaren Laboratory West Forvie Building, Robinson Way

department: Surgery

country: United Kingdom

institute: University of Cambridge

summary: We addressed the role of cell division during differentiation by blocking the progression of the cell cycle during mesendoderm differentiation. Human pluripotent stem cells (H9 cells) were synchronized in their cell cycle and then induced to differentiate into mesendoderm for 24h. To block the cells in their S phase, we added Hydroxyurea (200 uM) at the beginning of the differentiation process. To block the cells in their G2/M phases, we added nocodazole (100 ng/ml) 8h after the induction of differentiation. At the end of the experiment, the cells were harvested and processed for RNA extraction.

overall_design: Four different conditions were analyzed: Undifferentiated (UD), Mesendoderm (E24), Mesendoderm + Hydroxyurea (E24HU), and Mesendoderm + nocodazole (E24Noc). Two biological replicates were generated for each condition.


title: Effect of Cell Division on Cell Differentiation (RNA-Seq H9 cells UD E24 E24RO E24woTET E24TET)

summary: We addressed the role of cell cycle regulator CDK1 during differentiation by either inhibiting its activity with the specific inhibitor RO3306 (10µM) or by knocking its expression down using specific shRNAs, during mesendoderm differentiation. Human pluripotent stem cells (H9 cells) were synchronized in their cell cycle and then induced to differentiate into mesendoderm for 24h. shRNAs against CDK1 were induced 4 days before starting the differentiation. The CDK1 inhibitor was added to the medium 8h after the induction of differentiation. At the end of the experiment, the cells were harvested and processed for RNA extraction.

overall_design: Four different conditions were analyzed: Undifferentiated (UD), Mesendoderm (E24), Mesendoderm + CDK1 inhibityor (E24RO), Mesendoderm  without induction of shRNA_CDK1 with tetracycline (E24woTET), and Mesendoderm plus induction of shRNA_CDK1 with tetracycline (E2TET). Two biological replicates were generated for each condition.


title: Gene expression profiling of cerebellums in the central nervous system-specific Derlin-2 deficient mice

status: Public on May 28 2021

city: Miyazaki

first: Takashi

last: Sugiyama

address: 5200 Kihara, Kiyotake

department: Department of Medical Sciences

institute: University of Miyazaki

summary: To search gene expression change of cerebellum in the central nervous system-specific Derlin-2 mice, we performed genome-wide DNA microarray analysis and compared the expression levels between Derlin-2_control and Derlin-2_KO.

overall_design: Mice were sacrificed at postnatal day 28 by cervical dislocation and cerebellum was dissected for DNA microarray analysis.

first: Naoya

last: Murao

first: Hideki

last: Nishitoh


title: Transcriptomic changes associated with growth of Mycobacterium tuberculosis H37Rv wild-type strain and ∆prpR mutant in mineral medium supplemented with cholesterol as the sole carbon source or standard medium supplemented with vitamin B12.

city: Lodz

first: Jakub

last: Pawełczyk

address: Lodowa 106

department: Mycobacterium Physiology and Genetics

country: Poland

institute: Institute of Medical Biology of the Polish Academy of Sciences

summary: RNA-Seq results accompanying submission of a manuscript: "Cholesterol-dependent transcriptome remodeling reveals new insight into the contribution of cholesterol to Mycobacterium tuberculosis pathogenesis" describing the role of cholesterol and vitamin B12 in shaping the transcriptome of the Mycobacterium tuberculosis H37Rv and M. tuberculosis  ∆prpR - propionate regulator (PrpR) mutant. Next generation sequencing results are provided in  three independent biological replicates for each strain growing in three different media - minimal medium with glycerol or cholesterol as the sole carbon source and standard 7H9/10% OADC medium. The influence of vitamin B12 on M. tuberculosis transcriptome was analysed on 7H9/10% OADC medium supplemented with B12. The study allowed us to re-establish the list of genes potentially involved in cholesterol metabolism. We further proposed a novel regulatory function of vitamin B12 and PrpR, a propionate regulator, in coordinated cholesterol breakdown metabolite dissipation and virulent phenotype induction. Finally, we demonstrated that a key role of cholesterol in Mtb metabolism is not only providing carbon and energy but also inducing a transcriptome remodeling program that helps in developing tolerance to the unfavorable host cell environment.

overall_design: Next generation sequencing results are provided in  three independent biological replicates for each strain growing in three different media - minimal medium with 0.1% glycerol (vol/vol), minimal medium with 0.01% cholesterol (wt/vol) and standard 7H9/10% OADC medium. The influence of vitamin B12 on M. tuberculosis transcriptome was analysed on 7H9/10% OADC medium supplemented with B12 (10 μg/ml). For DGE analysis of bacteria grown in mineral medium with cholesterol, results obtained in medium with glycerol were treated as reference. For better specificity, the expression data for mineral medium with cholesterol were compared to the data obtained on standard  7H9/10% OADC medium. Only genes that were differentially expressed on cholesterol but NOT on 7H9/10% OADC were included to further studies and discussion. For the study on the role of vitamin B12 in shaping M. tuberculosis transcriptome the RNA-Seq analysis of the M. tuberculosis growing in 7H9/10% OADC medium supplemented with vitamine B12 was compared to the results obtained for M. tuberculosis growing in 7H9/10% OADC medium without B12 (reference).

first: Anna

last: Brzostek

first: Alina

last: Minias

first: Przemysław

last: Płociński

last: Rumijowska-Galewicz

first: Dominik

last: Strapagiel

first: Jolanta

last: Zakrzewska-Czerwińska

first: Jarosław

last: Dziadek


title: eNampt, CRH and Il-6 influence on gene expression of rat primary corticotropes.

city: Poznań

first: Marcin

last: Ruciński

state: Wielkopolska

address: Święcickiego 6

department: Histology and Embryology

institute: Poznań University of Medical Sciences

summary:
ACTH is known to be secreted from pituitary cortictropes after CRH and Il-6 stimulation. Recenetly it  was proven that eNampt also stimulates ACTH secretion from rat pituitary gland.
We used microarrays to detail the global programme of gene expression in isolated rat pituitary corticotropes, 24h after administration of eNampt, CRH and Il-6.

overall_design: Rat corticotropes were isolated from primary rat pituitary gland culture with anti-CRH antibody used as selection marker. Isolated Rat cortictropes were subjected to the cell culture. Subsequently eNampt, CRH and Il-6 were administered into the cell medium. After 24h, RNA were extracted and hybridize into the Affymetrix microarrays.

first: Piotr

last: Celichowski

first: Karol

last: Jopek

first: Marta

last: Szyszka

first: Paulina

last: Milecka

first: Marianna

last: Tyczewska

first: Svetlana

last: Sakhanova

first: Witold

last: Szaflarski

first: Ludwik

last: Malendowicz


title: IFN-b priming exacerbates LPS-driven proinflammatory cytokines in macrophages.

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
Purpose: We characterize the changes global expression profile in peripheral macrophages induced by LPS, IFN-b, and IFN-B+LPS treatment, using bulk RNA-sequencing.
Methods: mRNA profiles of bulk macrophages obtained from WT mice following treatment with either saline, IFN-b, LPS, or IFN-b+LPS.  Each treatment was performed in triplicate, and RNA-sequencing was performed on the Illumina 2500.  Reads passing quality metric were aligned to the mm10 genome using annotations produced by ENSEMBL, and were analyzed at the transcript level using one-way ANOVA and fold change requirements.
Results: We mapped approximately 20 million reads per sample to the mm10 genome, yielding 11385 reasonably-expressed transcripts.  We identified 4372 transcripts with a p-value<0.05 and fold change>2 when compared between LPS v NS, IFNb v NS, and LPS+IFNb v NS.  Of these, we identified 142 genes where priming by IFNb+LPS augmented the changes in expression induced by LPS or IFNb independently.  This gene set indicated that IFNb exacerbates LPS_driven proinflammatory cytokin production.
Conclusion: Here we show that IFNb priming sensitizes to TLD-driven inflammation through LPS stimulation.

overall_design: Our study characterizes the transcriptional changes induced by LPS, IFNb, and LPS+IFNb through RNAsequencing of peripheral macrophages.  Our results identify the augmentation of LPS-induced pathways through priming by IFNb.

first: Senad

last: Divanovic

first: Monica

last: Cappelleti


title: Expression data of Neutrophils treated with CTC Extracellular vesicles

status: Public on May 29 2021

city: Miami

first: Harrys Kishore

last: Charles Jacob

state: Florida

address: 1501 NW 10th Ave BRB 542E

institute: University of Miami, Miller SOM

summary: Circulating tumor cells (CTCs) found in the blood of pancreatic cancer patients show a worse prognosis to therapy if they are seen in clusters of cells with neutrophils or platelets or with other cell types than when they are seen as singlets. We wanted to investigate if there is a sec-ondary mode of communication between the CTCs and neutrophils that causes them to associ-ate. We describe for the first time an extravesicular (EV) mediated communication between CTCs and neutrophils that modulates early transcriptome changes that can cause neutrophils to partially degranulate and form associations. We also identify the protein cargo carried in such EVs and how when added to naïve neutrophils, they can modulate transcriptomic changes in neutrophils partially disarming them to form clusters rather than undergo specialized cell death, which is characterized by release of condensed chromatin (NETs) and granular contents termed as NETosis

overall_design: We used microarrays to detail the global programme of gene expression in neutrophils identifying neutrophil degranulation and reteplase activity being modulted on exposure to EVs from CTCs. Samples were collected at different minutes post exposure to EVs  and transcriptionally profiled to identify gene targets

first: Harrys

last: Jacob


title: scRNA-Seq of MDMX C462A and wildtype mice treated with acetaminophen

first: Zhi-Min

last: Yuan

summary: We report the application of scRNA sequencing technology for profiling of acetaminophen response in MDMXC462A mice. These data were used to evaluate differential gene expression and changes in cell composition using canonical markers for mouse liver cells.

overall_design: Examination of 2 different histone modifications in Neural progenitor cells.

first: Cb

last: Lim

first: Jiawei

last: Yan

first: Lizhen

last: Li

first: Monika

last: Lewinska

first: Cody

last: Rasmussen-Ivey

first: Jing

last: Jin


title: RNA sequencing of Bifidobacterium pseudocatenulatum MP80 grown on Lactose 2'-FL and LNFP-1

city: Davis

first: saumya

last: wickramasibnghe

state: CA

address: One Shields AVE

department: Food Science and Technology

institute: University of California Davis

summary: RNA sequencing revolutionized the bacterial gene expression analysis. The objective of this study was to identify the genes involved in metabolism of 2'-FL and LNFP1 in Bifidobacterium pseudocatenulatum MP80. We have obtained a list of genes upregulated in Bifidobacterium pseudocatenulatum MP80 when it is grown in 2% 2'-FL and LNFP1. Lactose grown samples were used as the control.

overall_design: Illumina RNAseq was conducted on RNA extracted from four samples of Bifidobacterium pseudocatenulatum MP80 (n=4) grown in 2% Lactose, four samples of Bifidobacterium pseudocatenulatum MP80 grown in 2% 2'-FL and four samples of Bifidobacterium pseudocatenulatum MP80 grown in 2% LNFP1. Samples were takin at the mid log phase of the growth curve.

first: David

middle: A

last: Mills

first: Britta

last: Heiss

first: Saumya

last: Wickramasinghe


title: Gene expression profiling of cerebellums in the central nervous system-specific Derlin-1 or Derlin-2 deficient mice

first: Takashi

last: Sugiyama

summary: To search gene expression change of cerebellum in the central nervous system-specific Derlin-1or Derlin-2 mice, we performed genome-wide DNA microarray analysis and compared the expression levels between Derlin-1_control and Derlin-1_KO. Furthermore, to search gene expression change of cerebellum the mice treated chemical chaperone, we compared the expression level among Derlin-1 or 2_control_vehicle, Derlin-1 or 2_control_4PBA, Derlin-1 or 2_KO_vehicle, and Derlin-1 or 2_KO_4PBA.

first: Naoya

last: Murao

first: Hideki

last: Nishitoh


title: The repertoire of newly developing regulatory T cells in the type I diabetes-prone NOD mouse is very diverse

city: Toulouse

first: Joost

last: van Meerwijk

address: CHU PURPAN

institute: INSERM CPTP

summary: Regulatory T lymphocytes expressing the forkhead/winged helix transcription factor Foxp3 (Treg) play a vital role in the protection of the organism from autoimmune disease and other immunopathologies. The antigen-specificity of Treg plays an important role in their in vivo activity. We therefore assessed the diversity of the T cell receptors for antigen (TCR) expressed by Treg newly developed in the thymus of autoimmune type I diabetes-prone NOD mice and compared it to the control mouse strain C57BL/6. Our results demonstrate that usage of the TCRα and TCRβ variable (V) and joining (J) segments, length of the complementarity determining region (CDR) 3, and the diversity of the TCRα and TCRβ chains are comparable between NOD and C57BL/6 mice. Genetic defects affecting the diversity of the TCR expressed by newly developed Treg therefore do not appear to be involved in the etiology of type I diabetes in the NOD mouse.

overall_design: We analyze the repertoire and TCR diversity from Tregs cells in the NOD mouse.

first: Ariel

last: Galindo-Albarran

first: Sarah

last: Castan

first: Jérémy

middle: C

last: Santamaria

first: Olivier

last: Joffre

first: Bart

last: Haegeman

first: Paola

last: Romagnoli

middle: P


title: Totipotency of mouse zygotes extends to single blastomeres of 4-cell stage embryos

status: Public on May 27 2021

city: Fukuoka

first: Yu-ichi

last: Tsukada

address: 744 Motooka, Fukuoka Nishi-ku

department: INAMORI Frontier Research Center Advanced Biological Information Research Division

institute: Kyushu University

summary: In multicellular organisms, heterogametes of oocytes and sperms are fertilized and resulting zygotes give rise to new individuals. The ability of zygotes that produce a fully formed individual from single cell when placed in a supportive environment is defined as totipotency. Given that totipotent cells are the source of all multicellular organisms, better understanding of totipotency has a profound effect on not only biology but also our society. However, the exact distribution of totipotent cells in mammals remains elusive, although zygotes and single blastomeres at 2-cell stage embryos has been thought to be only mouse cells to be totipotent. We now show that a single blastomere isolated from 2- and 4-cell stage embryos gives rise to a fertile adult individual when it placed in a uterus, although isolation of blastomeres at these stage results in the disturbance of transcriptome in single blastomere derived embryos. Single blastomeres from 8-cell and morula stage embryos that were separately cultured in vitro exhibited severe defects in the formation of epiblast and primitive endoderm in the inner cell mass and the development to blastocysts, respectively. Our results thus indicate that totipotency of mouse zygotes extends to single blastomeres of 4-cell stage embryos.

overall_design: Single-cell RNA sequencing of embryos with cavity derived from single blastomere of 1-, 2-, 4-, and 8-cell stage embryos.

first: Marino

last: Maemura

first: Hiroaki

last: Taketsuru

first: Yuki

last: Nakajima

first: Ruiqi

last: Shao

first: Ayaka

last: Kakihara

first: Jumpei

last: Nogami

first: Yasuyuki

last: Ohkawa


title: Positive natural selection of N6-methyladenosine on the RNAs of processed pseudogenes

city: Guangzhou

first: Liqiang

last: Tan

address: Zhongshan road 2,74

institute: Sun Yat-sen University

summary:
Background: Canonical Nonsense Mediated Decay (NMD) is an important splicing-dependent process for mRNA surveillance in mammals. However, processed pseudogenes are not able to trigger NMD due to their lack of introns. It is largely unknown whether they have evolved other surveillance mechanisms.
Results: Here, we find that the RNAs of pseudogenes, especially processed pseudogenes, have dramatically higher m6A levels than their cognate protein-coding genes, associated with de novo m6A peaks and motifs in human cells. Furthermore, pseudogenes have rapidly accumulated m6A motifs during evolution. The m6A sites of pseudogenes are evolutionarily younger than neutral sites and their m6A levels are increasing, supporting the idea that m6A on the RNAs of pseudogenes is under positive selection. We then find that the m6A RNA modification of processed, rather than unprocessed, pseudogenes promotes cytosolic RNA degradation and attenuates interference with the RNAs of their cognate protein-coding genes. We experimentally validate the m6A RNA modification of two processed pseudogenes, DSTNP2 and NAP1L4P1, which promotes the RNA degradation of both pseudogenes and their cognate protein-coding genes DSTN and NAP1L4. In addition, the m6A of DSTNP2 regulation of DSTN is partially dependent on the miRNA miR-362-5p.
Conclusions: Our discovery reveals a novel evolutionary role of m6A RNA modification in cleaning up the unnecessary processed pseudogene transcripts to attenuate their interfering with the regulatory network of proteincoding genes.

overall_design: mRNA profiles of control and siMETTL3 in GM12878 cells.

first: Weisheng

last: Cheng

first: Fang

last: Liu

first: Dan Ohtan

last: Wang

first: Linwei

last: Wu

last: Cao

first: Jinkai


title: Gene-regulatory network analysis of systemic lupus erythermatosus with a single-cell chromatin accessible assay

city: Shenzhen

first: Haiyan

last: YU

address: No. 1017, North of Dongmen Road

institute: Shenzhen People's Hospital

summary: Systemic lupus erythermatosus (SLE) is a complex autoimmune disease, and epigenetic study is promissing for illustrating the mechanisms of SLE pathogenesis. Assay for transposase accessible chromatin in single cells sequencing (scATAC-seq) shows priority to trackle this barrier. Thus, scATAC-seq was applied to difine the landscape of active regulatory DNA in systemic lupus erythermatosus (SLE) at single cell resolusion. Peripheral blood mononuclear cells (PBMCs) were robustly clustered based on their types without using antibodies. 20 patterns of transcription factor (TF) activation that drive abnormal immune response in SLE patients were identified. Meaniwhile, 10 genes associated with SLE pathogenesis that alter T cell activity and 52 significantly enriched TF motifs in SLE patients were revealed. These results reveal candidate makers in SLE-PBMC, showing feasibility for epigenetic therapy, and providing a foundational insights on epigenetic therapy.

overall_design: Single-cell chromatin accessibility (scATAC) profiles of human peripheral blood mononuclear cells in  systemic lupus erythermatosus

last: Yu

first: Hongwei

first: Yong

last: Dai


title: Extensive epigenetic priming in multipotent progenitors precedes lineage specification in B-lymphocyte development.

city: Lund

first: Mikael

last: Sigvardsson

address: Sölvegatan 19

country: Sweden

institute: Lund University

summary: B-lymphocyte development is dependent on the interplay between the chromatin landscape and lineage specific transcription factors. It has been suggested that B-lineage commitment is associated with major changes in the nuclear chromatin environment proposing a critical role for lineage specific transcription factors in the formation of the epigenetic landscape. In this report we have used chromosome conformation capture in combination with ATAC-seq analysis to enable highly efficient annotation of both proximal and distal transcriptional control elements to genes activated in B-lineage specification. A large majority of these genes were annotated to at least one regulatory element with an accessible chromatin configuration in multipotent progenitors. Furthermore, the majority of binding sites for the key regulators of B-lineage specification, EBF1 and PAX5,  occurred in already accessible regions. EBF1 did, however, cause a dynamic change in ATAC-accessibility and was critical for an increase in distal promoter-enhancer interactions as well as high deposition of chromatin modulating co-factors associated with the establishment of the B-lineage program. Our data unravel an unappreciated level of epigenetic priming at regulatory elements annotated to lineage restricted genes and provide insight into the mechanisms by which lineage specific transcription factors act via already accessible elements in lineage specification.

overall_design: Murine B-cell progenitor cells of Wt, Ebf1-KO, E2A-KO or Pax5-KO genotype or 230-238 B-cell progenitor cell line were  were subject to ATAC-seq, ChIP-seq and PLAC -seq analysis. ChIP-seq was performed as single or duplicate experiments, ATAC- and PLAC-seq as duplicates.

first: Tobias

last: Strid

first: Jonas

last: Ungerbäck

first: Kazuki

last: Okuyama

first: Mahadesh

last: Prasad

first: Rajesh

last: Somasundaram

first: Johanna

last: Tingvall-Gustafsson

first: Josefine

last: Åhsberg

first: Jacob

last: Kuruvilla

first: Christina

last: Jensen

first: Stefan

last: Lang

first: Susana

last: Cristobal

first: Shamit

last: Soneji


title: CoCl2 induced cytotoxicity is associated with dysregulated circRNAs and lncRNAs expression

first: Rui

last: Chen

address: 466 Xin Gang Zhong Road

department: Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute

institute: Guangdong Second Provincial General Hospital

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

overall_design: Refer to individual Series


title: Spike-in normalization for single-cell RNA-seq reveals dynamic global transcriptional activity mediating anti-cancer drug response

status: Public on May 25 2021

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

summary: The transcriptional plasticity of cancer cells promotes intercellular heterogeneity in response to anti-cancer drugs and facilitates the generation of subpopulation surviving cells. Characterizing single-cell transcriptional heterogeneity after drug treatments can provide mechanistic insights into drug efficacy. Here we used single-cell RNA sequencing (scRNA-seq) to examine transcriptomic profiles of cancer cells treated with chemotherapy drug paclitaxel, anti-inflammatory drug celecoxib, and the combination of the two drugs. By normalizing the expression of endogenous genes to spike-in molecules, we found that global mRNA abundance shows dynamic regulation across single cells after drug treatment. Using a random forest model, we identified gene signatures classifying single cells into three states: transcriptional repression, amplification, and control-like. Treatment with paclitaxel or celecoxib alone generally repressed gene transcription at variable levels across single cells. Interestingly, the combination of the two drugs resulted in transcriptional amplification and hyperactivation of the mitochondrial oxidative phosphorylation pathway, which is linked to enhanced cell killing efficiency. Finally, we identified a regulatory module enriched with metabolism and inflammatory genes that was activated in a subpopulation of paclitaxel-treated cells, the expression of which predicted paclitaxel efficacy across human cancer cell lines and in vivo patient samples. Our study highlights the dynamic global transcriptional activity driving single-cell heterogeneity during drug response. The results also emphasize the importance of adding spike-in molecules to study gene expression regulation using scRNA-seq experiments.

overall_design:
scRNA-seq of cancer cells treated with paclitaxel, celecoxib and the two drug combination

Please note that the Evalues.txt contains total 338 data columns as some bad quality samples were removed during the data analyses.

first: Vadim

last: Backman

first: Xin

last: Wang

first: Jane

last: Frederick


title: The impact of dietary cellulose on transcriptional profiles of colonic epithelial cells during inflammation.

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

institute: Philipps University Marburg

summary:
Purpose: Although dietary cellulose is considered health promoting, there is still a lack of understanding of cellular and molecular mechanisms. The aim of this study was to shed light on possible effects of the fiber on key players in intestinal homeostasis, including intestinal epithelial cells.
Method: Mice were fed a diet containing cellulose as the only source of fiber (CD, control diet) or a fiber free diet (FFD, fiber-free diet) for four weeks and then treated with dextran sulphate sodium in the drinking water for five days. To ensure that gene signatures were derived from colonic epithelial cells and not from contaminating lymphocytes, RAG1 KO mice deficient in intraepithelial lymphocytes were used.
Results: The analysis of differential expressed genes of colonic epithelial cells revealed multiple effects of dietary cellulose on the transcriptional profiles. In addition, cellulose caused a distinct clustering when comparing signature genes of different epithelial cell types.
Conclusion: This study demonstrated that dietary cellulose impacts transcriptional programs in colonic epithelial cells during inflammation.

overall_design: Colonic epithelial mRNA profiles of RAG1 KO mice receiving a cellulose-containing (n=5) and fiber-free diet (n=6) during inflammation.

first: Florence

last: Fischer

first: Ulrich

last: Steinhoff


title: MiRNA-sequencing in normal human epidermal melanocytes, melanoblast-related cells and melanoma cell lines

status: Public on May 26 2021

city: Regensburg

first: Norbert

last: Eichner

address: Universitätsstr. 31

institute: University of Regensburg

type: Non-coding RNA profiling by genome tiling array

summary: The study aims to identify differences in miRNA expression during melanoma development. Therefore, normal human epidermal melanocytes (NHEM) were de-differentiated into melanoblast-related cells (MBrCs) to model processes during embryonic differentiation and to compare them to the tumorigenic phenotype in melanoma development.

overall_design: Four different samples of NHEM from different passages, two independent replicates of MBrCs (the de-differentiation process is described in Cook et al. 2003, Journal of Investigative Dermatology) and the melanoma cell lines Mel Wei, Mel Ei, Mel Juso, Mel Ju, Mel Im and Hmb2 as well as Hmb2 cells (Hmb2-5) deficient for the melanoma tumor marker MIA (as described in Poser et al. 2004, Oncogene).

first: Lisa

last: Linck-Paulus

last: Lämmerhirt

first: Daniel

last: Völler

first: Anja

last: Bosserhoff

first: Gunter

last: Meister


title: Effect of Cell Division on Cell Differentiation

first: Rodrigo

last: Grandy


title: Small RNA, transcriptome and degradome analysis of the transgenerational heat stress response network in durum wheat

status: Public on May 24 2021

city: Urrbrae

first: Haipei

last: Liu

state: South Australia

address: PMB1 Waite Building, School AFW

country: Australia

institute: The University of Adelaide

summary: Heat stress is a major limiting factor for grain yield and grain quality in wheat production. In crops, abiotic stresses have transgenerational effects and the mechanistic basis of stress memory is associated with epigenetic regulation. The current study presents the first systematic analysis of the transgenerational effects of post-anthesis heat stress in tetraploid wheat. Genotype-dependent response patterns to parental and progeny heat stress were found for the leaf physiological traits, harvest components, and grain quality traits measured. Parental heat stress had positive influence on the offspring under re-occurring stress for traits like chlorophyll content, grain weight, grain number and grain total starch content. Integrated sequencing analysis of the small RNAome, mRNA transcriptome, and mRNA degradome provided the first description of the molecular networks mediating heat stress adaption under transgenerational influence. The expression profile of 1771 microRNAs (733 being novel) and 66,559 genes was provided, with differentially expressed microRNAs and genes identified subject to the progeny treatment, parental treatment and tissue type factors. Gene Ontology and KEGG pathway annotation of stress responsive microRNAs-mRNA modules provided further information on their functional roles in biological processes like hormone homeostasis, signal transduction, and protein stabilization. Our results provide new sights on the molecular basis of transgenerational heat stress adaptation, which can be used for improving thermos-tolerance in breeding.

overall_design: Analysis of small RNA transcriptome, mRNA transcriptome and mRNA degradome in eight biological pools (four treatment groups by two tissue types)

first: Amanda

last: Able

first: Jason


title: Single cell RNA-Seq profiling of MOVAS cells treated with cholesterol

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

country: Finland

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

summary: Mouse vascular smooth muscle cell line MOVAS cells were treated with cholesterol and analyzed by single-cell RNA-Seq to assess cell states.

overall_design: MOVAS cells treated with different concentrations of cholesterol were pooled into the scRNA-Seq run to capture the heterogeneity of the transcriptional states induced by cholesterol.

first: Kadri

last: Õunap

first: Minna

middle: U

last: Kaikkonen


title: ChIP-Seq of TRIB3 and ATF4 in HepG2 cells treated with bortezomib

city: Tartu

address: Riia 23b/2

department: Institute of Genomics

country: Estonia

institute: University of Tartu

summary: The proteasome is an appealing anti-cancer drug target and the proteasome inhibitor bortezomib has been approved for the treatment of certain types of malignancies. However, the molecular mechanisms underlying cancer cell resistance to bortezomib remain poorly understood. The pseudokinase TRIB3, an inhibitor of ATF4, is expressed at a high basal level in hepatoma cells and is strongly upregulated in response to bortezomib. To map genome-wide chromatin binding loci of TRIB3 protein, we fused a Flag tag to endogenous TRIB3 in HepG2 cells and performed ChIP-Seq. The results demonstrate that TRIB3 predominantly colocalizes with ATF4 on chromatin and the proteins reside in genomic regions containing the C/EBP-ATF motif. Bortezomib treatment leads to a robust enrichment of TRIB3 binding near genes induced by bortezomib and involved in the ER stress response and cell death. Disruption of TRIB3 increases C/EBP-ATF-driven transcription, augments ER stress and cell death in cells exposed to bortezomib, while TRIB3 overexpression enhances the cell survival. Thus, TRIB3, colocalizing with ATF4 and limiting its transcriptional activity, functions as a factor increasing resistance to bortezomib, while pharmacological over-activation of eIF2alpha-ATF4 can overcome the endogenous restraint mechanisms and sensitize cells to bortezomib.

overall_design: ChIP-Seq of Flag-tagged endogenous TRIB3 and endogenous ATF4 in HepG2 cells

first: Daima

first: Tõnis


title: Gene expression profiling of HepG2 cell response to bortezomib in combination with nelfinavir or ISRIB, compounds targeting the eIF2a-ATF4 pathway

summary: We investigate how modulation of the eIF2alpha-ATF4 stress pathway affects hepatoma cell response to bortezomib. Transcriptome profiling revealed that many ATF4 transcriptional target genes are among the highest upregulated genes in bortezomib-treated HepG2 human hepatoma cells. While pharmacological enhancement of the eIF2alpha-ATF4 pathway activity results in the elevation of the activities of all branches of the unfolded protein response (UPR) and sensitizes cells to bortezomib toxicity, the suppression of ATF4 induction delays bortezomib-induced cell death. The pseudokinase TRIB3, an inhibitor of ATF4, is expressed at a high basal level in hepatoma cells and is strongly upregulated in response to bortezomib. Bortezomib treatment leads to a robust enrichment of TRIB3 binding near genes induced by bortezomib and involved in the ER stress response and cell death. Disruption of TRIB3 increases C/EBP-ATF-driven transcription, augments ER stress and cell death in cells exposed to bortezomib, while TRIB3 overexpression enhances the cell survival. Thus, TRIB3, colocalizing with ATF4 and limiting its transcriptional activity, functions as a factor increasing resistance to bortezomib, while pharmacological over-activation of eIF2alpha-ATF4 can overcome the endogenous restraint mechanisms and sensitize cells to bortezomib.

overall_design: mRNA expression profiling of single-compound and combination treatments in HepG2 cells


title: RNA-seq analysis of Control and Mps1sKO testis at P10

city: shanghai

first: qiang

last: fang

address: 1239 Siping Road

institute: tongji university

summary: Monopolar spindle 1 (Mps1), which plays a critical role in somatic mitosis, has also been revealed to be essential for meiosis I in oocytes. Spermatogenesis is an important process involving successive mitosis and meiosis, but the function of Mps1 in spermatogenesis remains unclear. Here, we generated Mps1 conditional knockout mice and found that Ddx4-cre-driven loss of Mps1 in male mice resulted in depletion of undifferentiated spermatogonial cells and subsequently of differentiated spermatogonia and spermatocytes. In addition, Stra8-cre-driven ablation of Mps1 in male mice led to germ cell loss and fertility reduction. Spermatocytes lacking Mps1 were blocked at the zygotene-to-pachytene transition in prophase of meiosis I, and the expression of many meiotic genes was decreased, while that of apoptotic genes was increased. Moreover, we also detected increased apoptosis in spermatocytes with Mps1 knockout, which may have been the reason why germ cells were lost. Taken together, our findings indicate that Mps1 is required for mitosis of gonocytes and spermatogonia, differentiation of undifferentiated spermatogonia, and progression of meiosis I in spermatocytes.

overall_design: We sequenced the testis mRNA from both control mice and Mps1sKO mice at P10. Two biological replicates were generated per condition.

first: Qiang

last: Fang

first: Feng

last: Sun

first: Xiaomei

last: Yang


title: Genome-wide role of HSF1 in transcriptional regulation for desiccation tolerance of an anhydrobiotic cell line, Pv11

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

institute: Juntendo University

summary: Pv11 is an insect cell line established from Polypedilum vanderplanki with ability to survive complete desiccation if they were treated with trehalose. Previous studies showed contribution of HSF1 gene in this adaptation. To determine HSF1 regulatory network in Pv11 cells we prepared RNAseq libraries for wild type Pv11 (WT), HSF1 knoked out (Hsf1-/-), HSf1 resqued (Hsf1-/-; Hsf1-HaloTag/BlaR), and negative control for HSF1 resqued cells (Hsf1-/- HaloTag/BlaR) under normal conditions and under incubation with trehalose for 48 h. Comparison of mRNA profiles showed that HSF1 induced anhydrobiosis-related genes, especially LEA and TRX, but suppressed cellular process-related genes, for example transcription- and translation-related genes.

overall_design: Examination of expression profiles in 4 types of Pv11 cell cultures in 2 conditions.

first: Shoko

last: Tokumoto

first: Yugo

last: Miyata

first: Olga

last: Kozalova

first: Takahiro

last: Yamada

first: Yusuke

last: Hiki

first: Yuki

last: Yoshida

first: Richard

last: Cornette

first: Akira

last: Funahashi

first: Elena

last: Shagimardanova

first: Oleg

last: Gusev

last: Kikawada


title: total RNA-seq from heart right ventricle (ENCSR997KDB)

status: Public on May 23 2021

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
w73_heart_right_ventricle

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: Iron supplementation regulates the progression of high fat diet induced obesity and hepatic steatosis via mitochondrial signaling pathways [II]

city: Fujisawa

first: Naho

last: Kitamura

state: Kanagawa

department: Graduate School of Media and Governance

institute: Keio University

summary: Disruption of iron metabolism is closely related to metabolic diseases. Iron deficiency is frequently associated with obesity and hepatic steatosis. However, the effects of iron supplementation on obesity and energy metabolism remain unclear. Here we show that a high-fat diet supplemented with iron reduces body weight gain and hepatic lipid accumulation in mice. Iron supplementation was found to reduce mitochondrial morphological abnormalities and upregulate gene transcription involved in mitochondrial function and beta oxidation in the liver and skeletal muscle. In both these tissues, iron supplementation increased the expression of genes involved in heme or iron–sulfur (Fe–S) cluster synthesis. Heme and Fe–S cluster, which are iron prosthetic groups contained in electron transport chain complex subunits, are essential for mitochondrial respiration. The findings of this study demonstrated that iron regulates mitochondrial signaling pathways—gene transcription of mitochondrial component molecules synthesis and their energy metabolism. Overall, the study elucidates the molecular basis underlying the relationship between iron supplementation and obesity and hepatic steatosis progression, and the role of iron as a signaling molecule.

overall_design: Male C57BL/6J mice of 6 weeks of age were fed with a control diet (Control;10% kcal fat), a high-fat diet (HF; 60% kcal fat), or a high-fat diet supplemented with 0.023% (w/w) sodium ferrous citrate (HF+SFC) for 15 weeks. Control diet (D12450B) contained 10 kcal% fat, 20 kcal% protein, and 70 kcal% carbohydrate, whereas the HF diet (D12492) contained 60 kcal% fat, 20 kcal% protein, and 20 kcal% carbohydrate (Research Diets, Inc., New Brunswick, NJ, USA). For each group, a mix of all sample cDNAs was used.

first: Yoko

last: Yokoyama

first: Hiroki

last: Taoka

first: Utana

last: Nagano

first: Shotaro

last: Hosoda

first: Tanon

last: Taworntawat

first: Anna

last: Nakamura

last: Ogawa

first: Kazuo

last: Tsubota

first: Mitsuhiro

last: Watanabe


title: Skull and vertebral bone marrow are myeloid reservoirs for meninges and CNS parenchyma

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

summary: EAE is a chronic demyelinating condition characterized by central nervous system immune infiltration. Spinal cord injury results in damage to the spinal cord, partially due to leukocyte infiltration and inflammatory contributions. Here we performed single-cell RNA-sequencing of spinal cord tissue to examine how CNS-infiltrating cells from different niches may play distinct roles in different disease pathogenesis.

overall_design: Three pairs of female WT and UBC-GFP C57BL/6J mice were parabiotically joined at two months of age. Mice were allowed to recover for 60 days, where after experimental autoimmune encephalomyelitis (EAE) was induced in both pairs by MOG35-55 immunization. After 15 days, mice were sacrificed and spinal cord tissue was collected from the WT parabionts. In a separate experiment, four pairs of female WT and UBC-GFP C57BL/6J mice were parabiotically joined at two months of age. Mice were allowed to recover for 60 days, where after spinal cord injury was performed in both pairs by a T9 crush with fone forceps. After three days, mice were sacrificed and spinal cord tissue was collected from the WT parabionts. Tissues from both experiments were dissociated with collagenase 8 to obtain a single cell suspension and sorted by FACS based on the following phenotypes: DAPI- CD45hi IVCD45- GFP- or DAPI- CD45hi IVCD45- GFP+.

first: Tornike

last: Mamuladze

first: Justin

last: Rustenhoven

first: Andrea

last: Cugurra

first: Taitea

last: Dykstra


title: TF ChIP-seq from SK-N-SH (ENCSR969AIM)

summary:
eGFP-PATZ1 ChIP-seq on human SK-N-SH

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: Gene Expression profiling of Down Syndrome Lungs

city: Rochester

first: Soumyaroop

last: Bhattacharya

state: NY

address: 601 Elmwood Ave Box 703

department: Pediatrics

institute: University of Rochester

summary: Comprehensive gene expression assessment in prenatal DS lungs (n=19), and age-matched non-DS (n=19), was performed using high-throughput RNA sequencing (RNAseq)

overall_design: Assessment of gene expression changes in lungs from fetal samples with Trisomy 21

first: Denise

last: Al-Alam


title: total RNA-seq from foreskin keratinocyte (ENCSR959LTT)

first: ENCODE

last: DCC

summary:
RiboZero RNA-seq on primary keratinocytes in day 3 of differentiation

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 left cardiac atrium (ENCSR993IPO)

summary:
w78_left_cardiac_atrium

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: TF ChIP-seq from SK-N-SH (ENCSR949COJ)

summary:
eGFP-ARNTL ChIP-seq on human SK-N-SH

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: Onset of taste cell renewal starts at birth and coincides with a shift in SHH function

city: Philadelphia

first: Eric

last: Larson

state: PA

address: 240 S 40th St

institute: University of Pennsylvania

summary: RNAseq was employed to profile taste progenitors (SOX2-GFPhigh) and non-taste epithelial progenitors (SOX2-GFPlow) at the onset of taste cell renewal at birth. This dataset was acquired via FACS of SOX2-GFP+ epithelial cells from SOX2gfp/+ mouse pups at P0.

overall_design: P0 SOX2GFP cells were isolated from pooled lingual epithelium and separated by FACS.  Two populations (GFP-high, GFP-low) were collected for RNA extraction and sequencing.

first: Erin

last: Golden

middle: D

first: Linda

last: Barlow


title: Next Generation Sequencing of mRNA of cachectic mice muscles in C26 model

city: Nanjing

first: Shiyu

last: Song

state: China

address: Nanjing University, Nanjing, JiangSu Province, Kejiguan 210

institute: Nanjing University

summary: Cancer cachexia is a metabolic multifactorial syndrome that causes up to 20% of cancer-related deaths. Muscle atrophy, the hallmark of cancer cachexia, strongly impairs the quality of life of cancer patients; however, the underlying pathological process is still poorly understood. In our study, the transcriptome of cachectic gastrocnemius muscle in the C26 xenograft model was comparied with normal control. The key pathways involving this diseases was discovered according to the different expressed genes.

overall_design: Examination of the muscle of C26 baring mice and control mice

first: Mengyuan

last: Niu

first: Qian

last: Gao

first: Hongwei

last: Wang


title: TF ChIP-seq from K562 (ENCSR967AVR)

summary:
eGFP-ZBTB5 ChIP-seq on human 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: TF ChIP-seq from HepG2 (ENCSR932ZRD)

summary:
ChIP-Seq on HepG2

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: TF ChIP-seq from HepG2 (ENCSR944LSA)


title: total RNA-seq from heart right ventricle (ENCSR915EBZ)

summary:
w76_heart_right_ventricle

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: TF ChIP-seq from HepG2 (ENCSR945NSF)

summary:
PCBP2 ChIP-seq on HepG2

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: Histone ChIP-seq from fibroblast of lung (ENCSR915QOL)

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 activated T-cell (ENCSR900DUO)

summary:
Allcells13168 activated T-cells

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 heart left ventricle (ENCSR900FUP)

summary:
w73_heart_left_ventricle

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: TF ChIP-seq from SK-N-SH (ENCSR507BWM)

summary:
eGFP-GLIS3 ChIP-seq on human SK-N-SH

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 H1 (ENCSR895ZTB)

summary:
h1_hesc

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: TF ChIP-seq from HepG2 (ENCSR904JEY)


title: total RNA-seq from kidney (ENCSR892LBU)

summary:
w71_kidney

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: Histone ChIP-seq from WERI-Rb-1 (ENCSR967DBV)

summary:
H3K27me3 ChIP-seq on human WERI-Rb-1

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 upper lobe of left lung (ENCSR500JSJ)

summary:
W78_upper_lobe_of_left_lung

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: Iron supplementation regulates the progression of high fat diet induced obesity and hepatic steatosis via mitochondrial signaling pathways [I]

first: Naho

last: Kitamura

summary: Disruption of iron metabolism is closely related to metabolic diseases. Iron deficiency is frequently associated with obesity and hepatic steatosis. However, the effects of iron supplementation on obesity and energy metabolism remain unclear. Here we show that a high-fat diet supplemented with iron reduces body weight gain and hepatic lipid accumulation in mice. Iron supplementation was found to reduce mitochondrial morphological abnormalities and upregulate gene transcription involved in mitochondrial function and beta oxidation in the liver and skeletal muscle. In both these tissues, iron supplementation increased the expression of genes involved in heme or iron–sulfur (Fe–S) cluster synthesis. Heme and Fe–S cluster, which are iron prosthetic groups contained in electron transport chain complex subunits, are essential for mitochondrial respiration. The findings of this study demonstrated that iron regulates mitochondrial signaling pathways—gene transcription of mitochondrial component molecules synthesis and their energy metabolism. Overall, the study elucidates the molecular basis underlying the relationship between iron supplementation and obesity and hepatic steatosis progression, and the role of iron as a signaling molecule.

first: Yoko

last: Yokoyama

first: Hiroki

last: Taoka

first: Utana

last: Nagano

first: Shotaro

last: Hosoda

first: Tanon

last: Taworntawat

first: Anna

last: Nakamura

last: Ogawa

first: Kazuo

last: Tsubota


title: TF ChIP-seq from K562 (ENCSR899GSH)

last: DCC

summary:
RBM34 ChIP-seq 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: TF ChIP-seq from A549 (ENCSR886OEO)

summary:
EP300 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 mins.

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: Histone ChIP-seq from A549 (ENCSR480OHP)

summary:
H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 25 mins.

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: TF ChIP-seq from MCF-7 (ENCSR877UJB)

summary:
eGFP-ZNF227 ChIP-seq on human MCF-7

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: TF ChIP-seq from SK-N-SH (ENCSR474KBG)

summary:
eGFP-CSDC2 ChIP-seq on human SK-N-SH

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 excitatory neuron (ENCSR877FRY)

summary:
pgp1_excitatory_cortical_neuron

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 left ventricle myocardium superior (ENCSR876TAN)

summary:
w78_left_ventricle_myocardium_superior

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 heart left ventricle (ENCSR924MSZ)

summary:
w76_heart_left_ventricle

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: TF ChIP-seq from HepG2 (ENCSR882YYL)

summary:
ChIP-Seq on HepG2

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 right cardiac atrium (ENCSR867WQC)

summary:
w76_right_cardiac_atrium

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: Histone ChIP-seq from A549 (ENCSR864KVZ)

summary:
H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 20 mins.

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: TF ChIP-seq from A549 (ENCSR908AOO)

summary:
GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 15 mins.

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: Histone ChIP-seq from SU-DHL-6 (ENCSR471VHW)

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: TF ChIP-seq from MCF-7 (ENCSR860XVO)

summary:
eGFP-ZNF331 ChIP-seq on human MCF-7

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 right cardiac atrium (ENCSR853TXT)

summary:
w78_right_cardiac_atrium

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: TF ChIP-seq from brain (ENCSR467EQP)

summary:
CTCF ChIP-seq on brain female embryo (5 days)

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 lower lobe of left lung (ENCSR448BTT)

summary:
w78_left_lobe_of_lung

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: TF ChIP-seq from A549 (ENCSR471EKW)

summary:
GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 mins.

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 activated T-cell (ENCSR844SCP)

summary:
Allcells15824 activated T-cells

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: TF ChIP-seq from K562 (ENCSR850WUE)

summary:
RBM15 ChIP-seq 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: total RNA-seq from pancreas (ENCSR432EBE)

summary:
w73_pancreas

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: Histone ChIP-seq from lower leg skin (ENCSR432GOP)


title: total RNA-seq from endothelial cell (ENCSR429EGC)

summary:
pgp1_derived_endothelial_cells

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: TF ChIP-seq from SK-N-SH (ENCSR837YGS)

summary:
eGFP-ZNF608 ChIP-seq on human SK-N-SH

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: Histone ChIP-seq from gastrocnemius medialis (ENCSR423LXQ)


title: total RNA-seq from heart left ventricle (ENCSR837VMK)

summary:
w72_left_ventricle

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: TF ChIP-seq from K562 (ENCSR848AOP)

summary:
RBM22 ChIP-seq 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: total RNA-seq from mesenteric fat pad (ENCSR838XNO)

summary:
w73_mesenteric_fat_pad

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: TF ChIP-seq from K562 (ENCSR426PTT)

summary:
eGFP-FOXO4 ChIP-seq on human 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: total RNA-seq from lower lobe of right lung (ENCSR825UXP)

summary:
w78_lower_lobe_of_right_lung

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 (ENCSR820PHH)

summary:
GM12878

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 osteocyte (ENCSR413QAL)

summary:
H9 derived osteocytes

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 cardiac septum (ENCSR818DBU)

summary:
w61_cardiac_septum

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: TF ChIP-seq from HepG2 (ENCSR825MZS)

summary:
TAF15 ChIP-seq on HepG2

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: TF ChIP-seq from A549 (ENCSR857QEA)

summary:
GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 mins.

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 left lung (ENCSR410MSS)

summary:
w62_left_lung

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: TF ChIP-seq from A549 (ENCSR458VTP)

summary:
GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 20 mins.

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 upper lobe of right lung (ENCSR816IZA)

summary:
w78_upper_lobe_of_right_lung

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: TF ChIP-seq from K562 (ENCSR423FCW)

summary:
RBM14 ChIP-seq 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: total RNA-seq from left lung (ENCSR816HLU)

summary:
w76_left_lung

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: TF ChIP-seq from foreskin keratinocyte (ENCSR817HTJ)

summary:
CTCF ChIP-seq on primary keratinocytes in day 0 of differentiation

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 GM23338 (ENCSR379DEC)

summary:
pgp1_ipscs

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: Histone ChIP-seq from WERI-Rb-1 (ENCSR371OZG)

summary:
H3K9me3 ChIP-seq on human WERI-Rb-1

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 ovary (ENCSR368HRJ)

summary:
w80_ovary

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 left lobe of liver (ENCSR357BYU)

summary:
W82_left_lobe_of_liver

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 aorta (ENCSR377FPC)

summary:
w73_aorta

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 MCF-7 (ENCSR355JZC)

summary:
MCF-7_rep2

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 type B pancreatic cell (ENCSR352JCY)

summary:
H9 derived insulin producing beta-like cells

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: TF ChIP-seq from hepatocyte (ENCSR341VYI)

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: Histone ChIP-seq from OCI-LY7 (ENCSR347DAG)


title: TF ChIP-seq from A549 (ENCSR355HLV)

summary:
GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 mins.

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: TF ChIP-seq from K562 (ENCSR377BLZ)

summary:
GTF2F1 ChIP-seq 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: total RNA-seq from T-cell (ENCSR336VTK)

summary:
Allcells13168 inactive T-cells

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 mucosa of gallbladder (ENCSR343XXH)

summary:
W62_mucosa_of_gallbladder

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 (ENCSR797RXV)

summary:
IMR90_rep2

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: TF ChIP-seq from HepG2 (ENCSR799DUB)

summary:
ChIP-Seq on HepG2

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: TF ChIP-seq from foreskin keratinocyte (ENCSR812FNU)

summary:
CTCF ChIP-seq on primary keratinocytes in day 6 of differentiation

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 right lobe of liver (ENCSR323GUF)

summary:
w63_right_lobe_of_liver

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 ovary (ENCSR320OTJ)

summary:
w61_ovary

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: TF ChIP-seq from HepG2 (ENCSR804HMZ)

summary:
HNRNPLL ChIP-seq in HepG2

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: Histone ChIP-seq from A549 (ENCSR325VCV)

summary:
H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 15 mins.

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: TF ChIP-seq from SK-N-SH (ENCSR325QLX)

summary:
eGFP-ZNF8 ChIP-seq on human SK-N-SH

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: TF ChIP-seq from HepG2 (ENCSR315VYZ)


title: total RNA-seq from K562 (ENCSR792OIJ)

summary:
K562_rep_A

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: TF ChIP-seq from HepG2 (ENCSR339JTP)

summary:
RBM39 ChIP-seq in HepG2

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: Histone ChIP-seq from RWPE2 (ENCSR297ONS)

summary:
H3K4me3 ChIP-seq on human RWPE2

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 T-cell (ENCSR306IAW)

summary:
Allcells6054 inactive T-cells

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: Histone ChIP-seq from RWPE2 (ENCSR785DEU)

summary:
H3K9me3 ChIP-seq on human RWPE2

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: TF ChIP-seq from K562 (ENCSR791OZM)

summary:
RBM25 ChIP-seq 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: total RNA-seq from endodermal cell (ENCSR291TRJ)

summary:
H9 derived definitive endoderm

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: TF ChIP-seq from HepG2 (ENCSR313VZG)

summary:
FIP1L1 ChIP-seq on HepG2

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: TF ChIP-seq from A549 (ENCSR788VKG)

summary:
EP300 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 15 mins.

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 right cardiac atrium (ENCSR266PVZ)

summary:
w72_right_cardiac_atrium

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: TF ChIP-seq from SK-N-SH (ENCSR282NLQ)

summary:
eGFP-TSHZ2 ChIP-seq on human SK-N-SH

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 spleen (ENCSR258ELN)

summary:
w73_spleen

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: Histone ChIP-seq from RWPE2 (ENCSR784MON)

summary:
H3K27me3 ChIP-seq on human RWPE2

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 heart right ventricle (ENCSR252UHW)

summary:
w72_right_ventricle

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 adrenal gland (ENCSR763OMY)

summary:
w61_adrenal

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 left colon (ENCSR773COB)

summary:
w72_left_colon

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 neural crest cell (ENCSR761SHI)

summary:
H9 derived neural crest cells

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: TF ChIP-seq from HepG2 (ENCSR253HUM)

summary:
ChIP-Seq on HepG2

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: Histone ChIP-seq from A549 (ENCSR778NQS)

summary:
H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 mins.

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: TF ChIP-seq from smooth muscle cell (ENCSR261VAS)

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 HepG2 (ENCSR245ATJ)

summary:
HepG2_rep2

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 left colon (ENCSR759TPN)

summary:
w73_left_colon

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: TF ChIP-seq from H1 (ENCSR784VUY)


title: TF ChIP-seq from SK-N-SH (ENCSR758GOA)

summary:
eGFP-CREB5 ChIP-seq on human SK-N-SH

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: TF ChIP-seq from K562 (ENCSR268QIQ)

summary:
SRSF3 ChIP-seq 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: TF ChIP-seq from HepG2 (ENCSR288ZFV)

summary:
HepG2 immortalized cell line stably expressing C-terminal eGFP-ATF4 fusion protein.

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: TF ChIP-seq from SK-N-SH (ENCSR754GYI)

summary:
eGFP-BNC2 ChIP-seq on human SK-N-SH

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: TF ChIP-seq from SK-N-SH (ENCSR754ALX)

summary:
eGFP-ZNF565 ChIP-seq on human SK-N-SH

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: TF ChIP-seq from HepG2 (ENCSR243LNQ)

summary:
PRPF4 ChIP-seq on HepG2

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 right lobe of liver (ENCSR229LFK)

summary:
w62_right_lobe_of_liver

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 progenitor cell of endocrine pancreas (ENCSR733JBX)

summary:
H9 derived pancreatic progenitor cells

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 colonic mucosa (ENCSR202OWR)

summary:
w61_colon_mucosa

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: Histone ChIP-seq from A549 (ENCSR734FLK)

summary:
H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 mins.

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: TF ChIP-seq from SK-N-SH (ENCSR207GYC)

summary:
eGFP-ZNF70 ChIP-seq on human SK-N-SH

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: TF ChIP-seq from K562 (ENCSR214EKV)

summary:
eGFP-ZNF281 ChIP-seq on human 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: TF ChIP-seq from SK-N-SH (ENCSR226NRS)

summary:
eGFP-TOX2 ChIP-seq on human SK-N-SH

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: TF ChIP-seq from K562 (ENCSR220YXI)

summary:
PRPF4 ChIP-seq 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: TF ChIP-seq from K562 (ENCSR724GSW)

summary:
SAFB2 ChIP-seq 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: total RNA-seq from adrenal gland (ENCSR201XOZ)

summary:
W62_adrenal_gland

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: Histone ChIP-seq from HL-60 (ENCSR198IHT)

summary:
H3K27me3 ChIP-seq on human HL-60

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 lower lobe of left lung (ENCSR718RTN)

summary:
w73_lower_lobe_of_left_lung

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