title: Loss of the Caenorhabditis elegans pocket protein LIN-35 reveals  MuvB’s innate function as the repressor of DREAM target genes

city: Santa Cruz

first: Paul

last: Goetsch

address: 1156 High Street

department: MCD Biology

institute: UCSC

summary: The Retinoblastoma-like pocket proteins p130 and p107 act as gatekeepers of the cell cycle through their activity within the DREAM (Dp/Rb-like/E2F/MuvB) transcriptional repressor complex. The goal of this study was to address how the pocket protein contributes to DREAM complex assembly and function on chromatin by utilizing a protein null mutant of the only C. elegans pocket protein LIN-35. We performed ChIP-seq of C. elegans DRM subunits in wild-type and lin-35 null late embryos to assess the effect on their chromatin localization following loss of LIN-35.

overall_design:
Examination of 7 DRM complex subunits (DPL-1, EFL-1, LIN-35, LIN-9, LIN-37, LIN-52, and LIN-54) in lin-35(n745) (a protein null strain) and WT C. elegans late stage embryos to assess effects of loss of LIN-35 on DRM complex chromatin assembly.
Study includes reanalysis of GSM1195397 and GSM1195398 (GSE49204) with an additional replicate, generating the following processed data:
LIN-37.SDQ3166.N2.rep0.vsInputRep0.SES.bw
LIN-37.SDQ3166.N2.IDR.0.01.narrowPeak

first: Jacob

last: Garrigues

first: Susan

last: Strome


title: ChIP-seq from HepG2 (ENCSR868JLS)

status: Public on Oct 24 2017

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
U2AF1 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: ChIP-seq from uterus (ENCSR999QVR)

summary:
POLR2A ChIP-seq on human uterus

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


title: RNAseq of wild type and maternal-zygotic Nanog mutant (MZnanog) zebrafish embryos

status: Public on Oct 25 2017

city: Salt Lake City

first: James

middle: A

last: Gagnon

state: UT

address: 1390 Presidents Circle, Crocker Science Center Receiving, Crocker Science Center Receiving

department: Biological Sciences

institute: University of Utah

type: Expression profiling by high throughput sequencing

summary: Goal of this study is differential gene expression between wild type and MZnanog mutant during early zebrafish embryogenesis

overall_design: Three timepoints - 2 hours post fertilization (hpf), 4 hpf, and 6.5 hpf; two replicates of wild type at each time point, one replicate for MZnanog at each time point

first: Alexander

middle: F

last: Schier


title: ChIP-seq from stomach (ENCSR776AEL)

summary:
CTCF ChIP-seq on human stomach

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


title: ChIP-seq from MCF-7 (ENCSR866QPZ)

summary:
ATF7 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: ChIP-seq from esophagus muscularis mucosa (ENCSR862NOW)

summary:
Chip-Seq on muscle layer of esophagus

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


title: ChIP-seq from spleen (ENCSR999EPI)

summary:
ChIP-seq on human 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: ChIP-seq from HEK293 (ENCSR776LDJ)

summary:
eGFP-ZNF645 ChIP-seq on human HEK293 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: ChIP-seq from stomach (ENCSR775VUA)

summary:
POLR2A ChIP-seq on human stomach

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


title: ChIP-seq from tibial nerve (ENCSR999DEZ)

summary:
ChIP-seq on human tibial nerve

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


title: ChIP-seq from GM12878 (ENCSR861JUQ)

summary:
FOXK2 ChIP-seq on human 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: Hi-C from SJCRH30 (ENCSR998ZSP)

summary:
HiC experiment done on SJCRH30

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


title: ChIP-seq from HEK293 (ENCSR775HFF)

summary:
eGFP-ZNF791 ChIP-seq on human HEK293 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: ChIP-seq from gastrocnemius medialis (ENCSR998NQG)

summary:
CTCF ChIP-seq on human gastrocnemius medialis

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


title: Cis-regulatory landscape of four cell types of the retina

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

type: Methylation profiling by high throughput sequencing

summary: The retina is composed of ~50 cell-types with specific functions for the process of vision. Identification of the cis-regulatory elements active in retinal cell-types is key to elucidate the networks controlling this diversity. Here, we combined transcriptome and epigenome profiling to map the regulatory landscape of four cell-types isolated from mouse retinas including rod and cone photoreceptors as well as rare inter-neuron populations such as horizontal and starburst amacrine cells.  Integration of this information reveals sequence determinants and candidate transcription factors for controlling cellular specialization. Additionally, we refined parallel reporter assays to enable studying the transcriptional activity of large collection of sequences in individual cell-types isolated from a tissue.  We provide proof of concept for this approach and its scalability by characterizing the transcriptional capacity of several hundred putative regulatory sequences within individual retinal cell-types. This generates a catalogue of cis-regulatory regions active in retinal cell types and we further demonstrate their utility as potential resource for cellular tagging and manipulation.

sample_organism:
Mus musculus
synthetic construct
Adeno-associated virus

overall_design: We generated genome-wide DNA methylation maps of four cell types isolated from mouse retina using FACS-sorting isolated from transgenic animals carrying markers for cones, rods, HCs and SBACs. We used this information to design libraries of candidate CRE (based on hypomethylation-LMRs) that were cloned into a parallelized transcriptional reporter construct (PRA) and packaged in adeno-associated viruses (AAVs) for batch delivery into mouse eyes. We measured the activity of hundreds of CREs in the four individual cell types. Samples originate from starburst amacrine cells, cones, rods, horizontal cells and whole retina.

first: Dominik

last: Hartl

first: Arnaud

last: Krebs

first: Josephine

last: Juettner

first: Botond

last: Roska

last: Schübeler


title: ChIP-seq from esophagus squamous epithelium (ENCSR773JBP)

summary:
CTCF ChIP-seq on human esophagus squamous epithelium

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


title: ChIP-seq from HepG2 (ENCSR867VPL)

summary:
Control 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: ChIP-seq from vagina (ENCSR997NXO)

summary:
ChIP-seq on human vagina

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


title: ChIP-seq from transverse colon (ENCSR769WKR)

summary:
CTCF ChIP-seq on human transverse 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: ChIP-seq from K562 (ENCSR765SXU)

summary:
Input control ChIP-seq on human eGFP-FOXJ2 tagged K562 cell line.

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


title: ChIP-seq from breast epithelium (ENCSR986YXU)

summary:
ChIP-seq on human breast epithelium

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


title: ChIP-seq from breast epithelium (ENCSR774ONS)

summary:
Chip-Seq on -human (fragmentation date:Fri Nov 11 2016 00:00:00 GMT-0600 (CST)

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


title: ChIP-seq from subcutaneous adipose tissue (ENCSR762PCG)

summary:
CTCF ChIP-seq on human adipose tissue

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


title: ChIP-seq from Peyer's patch (ENCSR995QNB)

summary:
POLR2A ChIP-seq on human Peyer's patch

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


title: ChIP-seq from adrenal gland (ENCSR770IWO)

summary:
CTCF ChIP-seq on human 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: ChIP-seq from GM12878 (ENCSR987MTA)

summary:
BHLHE40 ChIP-seq on human 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: ChIP-seq from GM12878 (ENCSR859FDL)

summary:
ZNF687 ChIP-seq on human 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: ChIP-seq from suprapubic skin (ENCSR773QRB)

summary:
Chip-Seq on suprapubic skin

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


title: ChIP-seq from K562 (ENCSR997NGQ)

summary:
XRCC3 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: ChIP-seq from HEK293 (ENCSR985MYI)

summary:
eGFP-ZNF114 ChIP-seq on human HEK293 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: ChIP-seq from HEK293 (ENCSR767XSF)

summary:
eGFP-ZNF555 ChIP-seq on human HEK293 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: Hi-C from endothelial cell of hepatic sinusoid (ENCSR982KWR)

summary:
HiC experiment done on endothelial cell of hepatic sinusoid

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


title: ChIP-seq from transverse colon (ENCSR761RDB)

summary:
Chip-Seq on transverse 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: ChIP-seq from subcutaneous adipose tissue (ENCSR983SZL)

summary:
Chip-Seq on adipose tissue

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


title: ChIP-seq from sigmoid colon (ENCSR983XKG)

summary:
ChIP-seq on human sigmoid 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: ChIP-seq from HepG2 (ENCSR991ADX)

summary:
U2AF2 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: ChIP-seq from testis (ENCSR981CID)

summary:
CTCF ChIP-seq on human testis

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


title: ChIP-seq from HepG2 (ENCSR859JGF)

summary:
ATM ChIP-seq on human 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: ChIP-seq from HEK293T (ENCSR760UKJ)

summary:
ARNT ChIP-seq on human HEK293T

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


title: ChIP-seq from K562 (ENCSR979QYJ)

summary:
MNT 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: ChIP-seq from GM12878 (ENCSR764CZW)

summary:
ZNF217 ChIP-seq on human 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: ChIP-seq from MCF-7 (ENCSR761LRR)

summary:
ZNF512B 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: ChIP-seq from MCF-7 (ENCSR979FQP)

summary:
GATAD2B 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: ChIP-seq from HEK293 (ENCSR762DQP)

summary:
eGFP-ZNF658 ChIP-seq on human HEK293 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: ChIP-seq from subcutaneous adipose tissue (ENCSR980OPB)


title: ChIP-seq from HEK293 (ENCSR858FAN)

summary:
eGFP-ZNF621 ChIP-seq on human HEK293 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: ChIP-seq from suprapubic skin (ENCSR756KRS)

summary:
CTCF ChIP-seq on human suprapubic skin

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


title: ChIP-seq from body of pancreas (ENCSR979DMN)

summary:
POLR2A ChIP-seq on human body of 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: ChIP-seq from GM12878 (ENCSR976TBC)

summary:
IRF5 ChIP-seq on human 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: microRNA-seq from adrenal gland (ENCSR848SBA)

type: Non-coding RNA profiling by high throughput sequencing

summary:
miRNA-seq on human 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: ChIP-seq from 22Rv1 (ENCSR857PBV)

summary:
CTCF ChIP-seq on human 22Rv1

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


title: ChIP-seq from upper lobe of left lung (ENCSR976HZM)

summary:
Chip-Seq on -human (fragmentation date:Mon Sep 26 2016 00:00:00 GMT-0500 (CDT)

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


title: ChIP-seq from HEK293 (ENCSR751PNN)

summary:
eGFP-ZNF112 ChIP-seq on human HEK293 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: ChIP-seq from 22Rv1 (ENCSR847XGE)


title: ChIP-seq from MCF-7 (ENCSR757EMK)

summary:
SUZ12 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: ChIP-seq from vagina (ENCSR975QNR)

summary:
Chip-Seq on vagina

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


title: ChIP-seq from K562 (ENCSR975SSR)

summary:
eGFP-ELF1 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: ChIP-seq from sigmoid colon (ENCSR747VNS)

summary:
ChIP-seq on human sigmoid 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: ChIP-seq from GM12878 (ENCSR746XEG)

summary:
NFXL1 ChIP-seq on human 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: ChIP-seq from HEK293 (ENCSR978EQY)

summary:
eGFP-GLI2 ChIP-seq on human HEK293 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: ChIP-seq from esophagus squamous epithelium (ENCSR746FMO)

summary:
ChIP-seq on human esophagus squamous epithelium

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


title: ChIP-seq from HEK293 (ENCSR854ORP)

summary:
eGFP-ZNF350 ChIP-seq on human HEK293 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: ChIP-seq from ovary (ENCSR754DWU)

summary:
POLR2A ChIP-seq on human 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: ChIP-seq from K562 (ENCSR750LYM)

summary:
eGFP-NR2C2 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: ChIP-seq from K562 (ENCSR972ZBV)

summary:
ATF7 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: ChIP-seq from K562 (ENCSR754ZHU)

summary:
SNRNP70 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: ChIP-seq from body of pancreas (ENCSR853XCA)

summary:
ChIP-seq on human body of 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: ChIP-seq from tibial nerve (ENCSR846VRM)

summary:
Chip-Seq on -human (fragmentation date:Tue Nov 08 2016 00:00:00 GMT-0600 (CST)

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


title: ChIP-seq from K562 (ENCSR742IDN)

summary:
NR2C1 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: ChIP-seq from K562 (ENCSR845MXF)

summary:
Input control ChIP-seq on human eGFP-ADNP tagged K562 cell line.

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


title: ChIP-seq from gastroesophageal sphincter (ENCSR976KYQ)

summary:
Chip-Seq on -human (fragmentation date:Tue Sep 20 2016 00:00:00 GMT-0500 (CDT)

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


title: ChIP-seq from K562 (ENCSR849DZW)

summary:
Input control ChIP-seq on human eGFP-ZKSCAN8 tagged K562 cell line.

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


title: ChIP-seq from upper lobe of left lung (ENCSR972LYL)

summary:
CTCF ChIP-seq on human 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: ChIP-seq from lower leg skin (ENCSR978LBS)

summary:
ChIP-seq on human lower leg skin

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


title: ChIP-seq from thyroid gland (ENCSR975JIE)

summary:
ChIP-seq on human thyroid 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: ChIP-seq from K562 (ENCSR737UST)

summary:
eGFP-ZNF740 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: ChIP-seq from K562 (ENCSR740NPG)

summary:
eGFP-BACH1 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: ChIP-seq from ascending aorta (ENCSR960MDF)

summary:
CTCF ChIP-seq on human ascending 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: ChIP-seq from MCF-7 (ENCSR965XFJ)

summary:
Input control ChIP-seq on human eGFP-CEBPG tagged MCF7 cell line.

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


title: ChIP-seq from K562 (ENCSR966DOU)

summary:
Control 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: ChIP-seq from transverse colon (ENCSR974HQI)

summary:
POLR2A ChIP-seq on human transverse 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: microRNA-seq from GM23338 (ENCSR958UOC)

summary:
miRNA-seq on human induced pluripotent stem cell

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


title: ChIP-seq from stomach (ENCSR955OCL)

summary:
ChIP-seq on human stomach

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


title: ChIP-seq from thyroid gland (ENCSR744YJR)

summary:
CTCF ChIP-seq on human thyroid 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: ChIP-seq from thyroid gland (ENCSR955BIB)


title: ChIP-seq from esophagus squamous epithelium (ENCSR734ZOZ)

summary:
POLR2A ChIP-seq on human esophagus squamous epithelium

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


title: ChIP-seq from K562 (ENCSR847LBF)

summary:
eGFP-FOXJ2 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: microRNA-seq from midbrain (ENCSR835AJS)

summary:
miRNA-seq on embryonic 10.5 day mouse midbrain

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


title: ChIP-seq from HepG2 (ENCSR748EXO)

summary:
Control 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: ChIP-seq from esophagus muscularis mucosa (ENCSR834ESZ)

summary:
ChIP-seq on human esophagus muscularis 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: ChIP-seq from upper lobe of left lung (ENCSR970UZD)

summary:
CTCF ChIP-seq on human 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: Hi-C from astrocyte of the spinal cord (ENCSR974LXZ)

summary:
HiC experiment done on astrocyte of the spinal cord

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


title: ChIP-seq from K562 (ENCSR969FPP)

summary:
Input control ChIP-seq on human eGFP-BACH1 tagged K562 cell line.

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


title: ChIP-seq from GM12878 (ENCSR732PJX)

summary:
NKRF ChIP-seq on human 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: ChIP-seq from HepG2 (ENCSR968QDP)

summary:
SMARCE1 ChIP-seq on human 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: ChIP-seq from HepG2 (ENCSR950NAZ)

summary:
LCORL ChIP-seq on human 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: ChIP-seq from K562 (ENCSR845BCL)

summary:
eGFP-ZNF639 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: ChIP-seq from K562 (ENCSR744WOO)

summary:
TCF12 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: ChIP-seq from GM12878 (ENCSR841NDX)

summary:
ELF1 ChIP-seq on human 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: ChIP-seq from K562 (ENCSR832OGB)

summary:
LEF1 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: ChIP-seq from MCF-7 (ENCSR966YYJ)

summary:
BMI1 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: ChIP-seq from upper lobe of left lung (ENCSR964BKO)


title: ChIP-seq from HEK293 (ENCSR736ZKL)

summary:
eGFP-ZNF148 ChIP-seq on human HEK293 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: ChIP-seq from omental fat pad (ENCSR846TPT)

summary:
Chip-Seq on adipose tissue of omentum

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


title: ChIP-seq from upper lobe of left lung (ENCSR961NYO)

summary:
ChIP-seq on human 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: ChIP-seq from K562 (ENCSR836COE)

summary:
RBM17 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: ChIP-seq from HepG2 (ENCSR735QJO)

summary:
Control 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: ChIP-seq from esophagus squamous epithelium (ENCSR838RUX)

summary:
CTCF ChIP-seq on human esophagus squamous epithelium

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


title: ChIP-seq from K562 (ENCSR829NNQ)

summary:
Input control ChIP-seq on human eGFP-ZNF766 tagged K562 cell line.

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


title: ChIP-seq from subcutaneous adipose tissue (ENCSR956TLA)

summary:
Chip-Seq on -human (fragmentation date:Tue Aug 30 2016 00:00:00 GMT-0500 (CDT)

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


title: ChIP-seq from testis (ENCSR953MEE)

summary:
ChIP-seq on human testis

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


title: ChIP-seq from prostate gland (ENCSR829HTO)

summary:
CTCF ChIP-seq on human prostate 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: ChIP-seq from K562 (ENCSR943AOR)

summary:
Input control ChIP-seq on human eGFP-USF2 tagged K562 cell line.

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


title: ChIP-seq from upper lobe of left lung (ENCSR828PZH)

summary:
Chip-Seq on 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: ChIP-seq from tibial nerve (ENCSR935XOT)

summary:
POLR2A ChIP-seq on human tibial nerve

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


title: ChIP-seq from 22Rv1 (ENCSR933UGQ)

summary:
ChIP-seq on human 22Rv1

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


title: ChIP-seq from HEK293T (ENCSR831EIW)

summary:
FOXM1 ChIP-seq on human HEK293T

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


title: ChIP-seq from K562 (ENCSR729HVR)

summary:
eGFP-ZNF644 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: ChIP-seq from K562 (ENCSR832DMO)

summary:
SRSF1 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: ChIP-seq from K562 (ENCSR948KMB)

summary:
PTBP1 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: ChIP-seq from MCF-7 (ENCSR949IWY)

summary:
PAX8 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: ChIP-seq from breast epithelium (ENCSR728WVG)

summary:
Chip-Seq on -human (fragmentation date:Fri Nov 11 2016 00:00:00 GMT-0600 (CST)

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


title: Hi-C from SK-N-MC (ENCSR834DXR)

summary:
HiC experiment done on SK-N-MC

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


title: ChIP-seq from transverse colon (ENCSR833FWC)

summary:
CTCF ChIP-seq on human transverse 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: ChIP-seq from suprapubic skin (ENCSR827FNU)

summary:
ChIP-seq on human suprapubic skin

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


title: ChIP-seq from spleen (ENCSR728EBP)

summary:
ChIP-seq on human 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: microRNA-seq from heart (ENCSR832SAG)

summary:
miRNA-seq on embryonic 12.5 day mouse heart

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


title: ChIP-seq from sigmoid colon (ENCSR925GDS)

summary:
CTCF ChIP-seq on human sigmoid 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: ChIP-seq from GM12878 (ENCSR828NCB)

summary:
GATAD2B ChIP-seq on human 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: ChIP-seq from HEK293 (ENCSR728MWW)

summary:
eGFP-ZIC2 ChIP-seq on human HEK293 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: ChIP-seq from HEK293 (ENCSR950ACO)

summary:
eGFP-ZNF785 ChIP-seq on human HEK293 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: ChIP-seq from HEK293 (ENCSR727PIC)

summary:
eGFP-ZNF34 ChIP-seq on human HEK293 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: ChIP-seq from upper lobe of left lung (ENCSR949XFR)

summary:
Chip-Seq on -human (fragmentation date:Mon Sep 26 2016 00:00:00 GMT-0500 (CDT)

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


title: ChIP-seq from HEK293 (ENCSR731AGO)

summary:
eGFP-ZSCAN5CP ChIP-seq on human HEK293 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: ChIP-seq from HepG2 (ENCSR730TBC)

summary:
MNT ChIP-seq on human 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: ChIP-seq from MCF-7 (ENCSR924TVL)

summary:
RFX5 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: ChIP-seq from spleen (ENCSR729GXE)

summary:
POLR2A ChIP-seq on human 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: ChIP-seq from uterus (ENCSR948PSS)

summary:
ChIP-seq on human uterus

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


title: ChIP-seq from SK-N-SH (ENCSR945NFL)

summary:
USF2 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: ChIP-seq from K562 (ENCSR932KYH)

summary:
Control 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: ChIP-seq from transverse colon (ENCSR930CPA)

summary:
Chip-Seq on transverse 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: ChIP-seq from MCF-7 (ENCSR931XKA)

summary:
Input control ChIP-seq on human eGFP-KLF9 tagged MCF7 cell line.

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


title: ChIP-seq from suprapubic skin (ENCSR928LDG)

summary:
Chip-Seq on suprapubic skin

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


title: ChIP-seq from suprapubic skin (ENCSR825RBI)

summary:
POLR2A ChIP-seq on human suprapubic skin

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


title: ChIP-seq from K562 (ENCSR825KUF)

summary:
Input control ChIP-seq on human eGFP-CEBPG tagged K562 cell line.

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


title: ChIP-seq from tibial nerve (ENCSR822PJT)

summary:
CTCF ChIP-seq on human tibial nerve

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


title: ChIP-seq from lower leg skin (ENCSR727HME)

summary:
CTCF ChIP-seq on human lower leg skin

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


title: ChIP-seq from stomach (ENCSR823FFR)

summary:
Chip-Seq on stomach

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


title: ChIP-seq from sigmoid colon (ENCSR923WJS)

summary:
Chip-Seq on sigmoid 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: ChIP-seq from sigmoid colon (ENCSR724FCJ)

summary:
POLR2A ChIP-seq on human sigmoid 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: ChIP-seq from K562 (ENCSR822LBD)

summary:
RBFOX2 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: ChIP-seq from HEK293T (ENCSR821YOI)

summary:
ChIP-seq on human HEK293T

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


title: ChIP-seq from HEK293 (ENCSR721QZV)

summary:
eGFP-ZSCAN18 ChIP-seq on human HEK293 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: ChIP-seq from GM12878 (ENCSR725VFL)

summary:
TCF12 ChIP-seq on human 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: ChIP-seq from K562 (ENCSR924GXX)

summary:
PHB2 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: ChIP-seq from K562 (ENCSR822DUK)

summary:
Input control ChIP-seq on human eGFP-ZNF740 tagged K562 cell line.

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


title: ChIP-seq from sigmoid colon (ENCSR721AHD)

summary:
CTCF ChIP-seq on human sigmoid 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: ChIP-seq from GM12878 (ENCSR822AHX)

summary:
IKZF2 ChIP-seq on human 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: ChIP-seq from esophagus muscularis mucosa (ENCSR922GUA)

summary:
POLR2A ChIP-seq on human esophagus muscularis 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: ChIP-seq from MCF-7 (ENCSR725ELR)

summary:
LARP7 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: ChIP-seq from lower leg skin (ENCSR821NQM)

summary:
ChIP-seq on human lower leg skin

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


title: ChIP-seq from spleen (ENCSR819SSW)

summary:
ChIP-seq on human 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: microRNA-seq from forebrain (ENCSR715QTV)

summary:
miRNA-seq on embryonic 12.5 day mouse forebrain

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


title: microRNA-seq from limb (ENCSR715NEZ)

summary:
miRNA-seq on embryonic 10.5 day mouse limb

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


title: ChIP-seq from HepG2 (ENCSR923UTX)

summary:
NONO 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: ChIP-seq from K562 (ENCSR814CUB)

summary:
Input control ChIP-seq on human eGFP-ZBTB11 tagged K562 cell line.

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


title: ChIP-seq from Peyer's patch (ENCSR921JFJ)

summary:
ChIP-seq on human Peyer's patch

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


title: ChIP-seq from K562 (ENCSR817QKV)

summary:
EP400 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: ChIP-seq from MCF-7 (ENCSR713NUS)

summary:
Input control ChIP-seq on human eGFP-E2F4 tagged MCF7 cell line.

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


title: ChIP-seq from K562 (ENCSR920ASP)

summary:
eGFP-ZFX 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: ChIP-seq from HEK293 (ENCSR811JJM)

summary:
eGFP-ZNF19 ChIP-seq on human HEK293 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: microRNA-seq from heart (ENCSR912ATB)

summary:
miRNA-seq on embryonic 10.5 day mouse heart

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


title: ChIP-seq from esophagus squamous epithelium (ENCSR710DTC)

summary:
ChIP-seq on human esophagus squamous epithelium

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


title: ChIP-seq from prostate gland (ENCSR911JAX)

summary:
POLR2A ChIP-seq on human prostate 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: ChIP-seq from right lobe of liver (ENCSR911GFJ)

summary:
CTCF ChIP-seq on human 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: ChIP-seq from gastrocnemius medialis (ENCSR915QUT)

summary:
ChIP-seq on human gastrocnemius medialis

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


title: ChIP-seq from K562 (ENCSR807BGP)

summary:
MTA1 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: ChIP-seq from GM12878 (ENCSR706YUH)

summary:
SMARCA5 ChIP-seq on human 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: ChIP-seq from K562 (ENCSR709DRM)

summary:
eGFP-E2F5 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: ChIP-seq from prostate gland (ENCSR720USO)

summary:
CTCF ChIP-seq on human prostate 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: ChIP-seq from K562 (ENCSR914NEI)

summary:
MTA3 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: ChIP-seq from VCaP (ENCSR716BTZ)

summary:
ChIP-seq on human VCaP

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


title: ChIP-seq from sigmoid colon (ENCSR906UPC)

summary:
Chip-Seq on sigmoid 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: ChIP-seq from suprapubic skin (ENCSR915TAF)

summary:
Chip-Seq on -human (fragmentation date:Mon Sep 12 2016 00:00:00 GMT-0500 (CDT)

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


title: ChIP-seq from stomach (ENCSR714JRB)

summary:
Chip-Seq on stomach

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


title: ChIP-seq from transverse colon (ENCSR717TBA)

summary:
Chip-Seq on -human (fragmentation date:Wed Aug 24 2016 00:00:00 GMT-0500 (CDT)

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


title: ChIP-seq from testis (ENCSR803FAP)

summary:
POLR2A ChIP-seq on human testis

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


title: ChIP-seq from MCF-7 (ENCSR814KDE)

summary:
Input control ChIP-seq on human eGFP-GABPA tagged MCF7 cell line.

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


title: ChIP-seq from transverse colon (ENCSR714EQS)

summary:
Chip-Seq on transverse 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: ChIP-seq from transverse colon (ENCSR704IJM)


title: ChIP-seq from prostate gland (ENCSR912ZIY)

summary:
Chip-Seq on prostate

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


title: ChIP-seq from HEK293 (ENCSR701RXW)

summary:
eGFP-ZNF530 ChIP-seq on human HEK293 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: ChIP-seq from K562 (ENCSR911VTL)

summary:
Input control ChIP-seq on human eGFP-ZNF644 tagged K562 cell line.

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


title: ChIP-seq from HEK293 (ENCSR801BWR)

summary:
eGFP-ZNF155 ChIP-seq on human HEK293 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: ChIP-seq from MCF-7 (ENCSR907JTZ)

summary:
Input control ChIP-seq on human eGFP-FOSL2 tagged MCF7 cell line.

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


title: ChIP-seq from K562 (ENCSR711VWL)

summary:
HDAC1 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: ChIP-seq from MCF-7 (ENCSR810WXH)

summary:
TOE1 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: ChIP-seq from epithelial cell of prostate (ENCSR910PDW)

summary:
H3K27ac ChIP-seq on human epithelial cell of prostate

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


title: ChIP-seq from K562 (ENCSR710WLO)

summary:
MGA 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: ChIP-seq from MCF-7 (ENCSR801SWX)

summary:
TARDBP 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: ChIP-seq from K562 (ENCSR805ITZ)

summary:
Input control ChIP-seq on human eGFP-NR2C1 tagged K562 cell line.

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


title: ChIP-seq from stomach (ENCSR804FRO)

summary:
Chip-Seq on -human (fragmentation date:Tue Aug 30 2016 00:00:00 GMT-0500 (CDT)

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


title: Transcriptome and translatome profiling from brains of  a mouse model of severe SMA

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

summary:
Spinal muscular atrophy (SMA) is the most common genetic cause of infant mortality, with an incidence of around 1 in 6,000-10,000 live births. SMA is caused by low levels of full-length survival of motor neuron protein (SMN). Approximately 95% of SMA cases in humans are caused by homozygous deletion of SMN1, with a smaller number caused by discrete mutations within the gene. In concert with other RNA binding proteins, SMN forms complexes both in the nucleus and the cytoplasm of neurons. As such, SMN protein has housekeeping roles in the assembly of ribonucleoprotein (RNP) complexes. In addition, SMN localises to dendrites, synapses and axons in vivo and in vitro, where it is part of messenger RNP (mRNP) complexes with well-known roles in the transport of mRNA. These cellular processes are tightly linked to local translation, suggesting that SMN may play a pivotal role in its regulation. We employed next generation sequencing (NGS) to identify and quantify RNAs associated with polysomes (POL-Seq) in parallel with total cytoplasmic RNA (RNA-Seq) in an established mouse model of severe SMA at both early and late-symptomatic stages. This approach enables the simultaneous identification of variations in RNA populations at both translatome (RNAs engagement with polysomes) and transcriptome (steady state cytoplasmic RNAs) levels.
Keywords: motor neuron disease, spinal muscular atrophy, SMA,SMN, translation, polysome profiling, POL-Seq, RNA-Seq

overall_design: We extracted both total cytoplasmic and polysomal RNAs from pooled sucrose fractions from early-symptomatic and late-symptomatic brains of SMA mice, as well as from littermate controls. Experiments were performed in biological triplicate for late-symptomatic mice, and in biological duplicate for early-symptomatic mice, for a total of 20 samples.

first: Paola

last: Bernabò

first: Ewout

middle: J

last: Groen

first: Elena

last: Perenthaler

last: Zuccotti

first: Alessandro

last: Quattrone

first: Thomas

middle: H

last: Gillingwater

first: Gabriella

last: Viero


title: microRNA-seq from heart left ventricle (ENCSR705STY)

last: DCC

summary:
miRNA-seq on human 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: microRNA-seq from vagina (ENCSR913DCT)

summary:
miRNA-seq on human vagina

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


title: ChIP-seq from HEK293T (ENCSR906PEI)

summary:
SP1 ChIP-seq on human HEK293T

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


title: ChIP-seq from spleen (ENCSR800BRO)

summary:
ChIP-seq on human 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: Genome-wide analysis of the auxin/indoleacetic acid (Aux/IAA) gene family in allotetraploid rapeseed (Brassica napus L.)

status: Public on Oct 23 2017

city: Wuhan

first: Bo

last: Wang

state: Hubei

address: No.1,Shizishan Street

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agricultural University

summary: Background: Auxin/Indoleacetic acid (Aux/IAA) genes participate in the auxin signaling pathway and play key roles in plant growth and development. Although the Aux/IAA gene family has been identified in many plants, within allotetraploid Brassica napus little is known.   Results: In this study, a total of 119 Aux/IAA genes were found in the genome of B. napus. They were distributed non-randomly across all 19 chromosomes and other non-anchored random scaffolds, with a symmetric distribution in the A and C subgenomes. Evolutionary and comparative analysis revealed that 111 (94.1%) B. napus Aux/IAA genes were multiplied due to ancestral Brassica genome triplication and recent allotetraploidy from B. rapa and B. oleracea. Phylogenetic analysis indicated seven subgroups containing 29 orthologous gene sets and two Brassica-specific gene sets. Structures of genes and proteins varied across different genes but were conserved among homologous genes in B. napus. Furthermore, analysis of transcriptional profiles revealed that the expression patterns of Aux/IAA genes in B. napus were tissue dependent. Auxin-responsive elements tend to be distributed in the proximal region of promoters, and are significantly associated with early exogenous auxin up-regulation.   Conclusions: The Aux/IAA gene family were identified and analyzed comprehensively in the allotetraploid B. napus genome. This analysis provides a deeper understanding of diversification of Aux/IAA gene family and will facilitate further dissection of Aux/IAA gene function in B. napus.

overall_design: Examination of the auxin response of gene exoression in Brassica napus seedling

first: Haitao

last: Li

first: Qinghua

last: Zhang

first: Jing

first: Graham

last: King

first: Kede

last: Liu


title: ChIP-seq from gastroesophageal sphincter (ENCSR906OMM)

first: ENCODE

summary:
Chip-Seq on esophagogastric junction

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


title: ChIP-seq from K562 (ENCSR706BJO)

summary:
eGFP-ZBTB11 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: ChIP-seq from HEK293 (ENCSR906PCS)

summary:
eGFP-ZNF223 ChIP-seq on human HEK293 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: ChIP-seq from MCF-7 (ENCSR702BYX)

summary:
NFIB 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: A bacterial receptor PcrK senses the plant hormone cytokinin to promote adaptation to oxidative stress

city: Beijing

first: Wang

last: Fang-Fang

address: Chaoyang District, Beichen West Road, No. 1 yard

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: By analyzing the transcriptome of WT/ΔpcrR/ΔpcrK strains in the presence of 2iP and comparing gene expression level between them, we report genes with different expression levels between WT and ΔpcrR/ΔpcrK strains in the presence of plant cytokinin 2iP.

overall_design: Transcriptome profile of all three strains were generated by high-throughput sequencing, Illumina Hiseq 2000

first: Fang-Fang

first: Wei

last: Qian


title: Type I interferon signaling attenuates Regulatory T cells function in viral infection and in the tumor microenvironment

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

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

overall_design: Refer to individual Series


title: H3K27me3 dynamics dictate evolving uterine states in pregnancy and parturition [RNA-seq]

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: Uncovering the causes of pregnancy complications such as preterm labor requires greater insight into how the uterus remains in a non-contractile state until term and then surmounts this state to enter labor. Here, we show in mice that dynamic deposition and removal of repressive H3K27me3 chromatin marks in decidual stromal cells dictate both elements of pregnancy success. In early gestation, H3K27me3-induced transcriptional silencing of select gene targets insures uterine quiescence by preventing the decidua from expressing parturition-inducing hormone receptors, manifesting type 1 immunity, and, most unexpectedly, generating myofibroblasts and associated wound healing responses. In late gestation, genome-wide H3K27 demethylation allows for target gene upregulation, decidual activation, and labor entry. Strikingly, pharmacological inhibition of this latter process not only prevented term parturition, but also inhibited delivery while maintaining pup viability in a non-inflammatory model of preterm parturition. Immunofluorescence analysis of human specimens suggested that similar regulatory events might occur in the human decidua. Together, these results reveal the centrality of regulated gene silencing in the uterine adaptation to pregnancy and suggest new areas in the study and treatment of pregnancy disorders.

overall_design: RNA-Seq was performed on stromal cells purified from different uterine tissue layers and cultured for 24 prior to analysis.  Biological replicates (1-3) are indicated.

first: Patrice

last: Nancy

first: Johan

last: Siewiera

first: Adrian

last: Erlebacher


title: Suppression of adaptive responses to targeted cancer therapy by transcriptional repression [RNA-seq]

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Large-scale genomic profiling efforts have facilitated the characterization of molecular alterations in cancers and aided the development of targeted kinase inhibitors for a wide array of cancer types. However, resistance to these targeted therapies invariably develops and limits their clinical efficacy. Targeting tumours with kinase inhibitors induces complex adaptive survival programs that promote the persistence of a fraction of the original cancer cell population, facilitating the eventual outgrowth of inhibitor-resistant tumour clones following clonal evolution. Here we show that the addition of a newly identified transcriptional repressor, THZ1, to targeted cancer therapy enhances cell killing and impedes the emergence of drug-resistant cell populations in cellular and in vivo cancer models with diverse genetic dependencies. We propose that targeted therapy induces a state of transcriptional dependency in a subpopulation of cells poised to become drug tolerant. THZ1 can exploit this dependency by blocking dynamic transcriptional responses, remodelling of enhancers and key signalling outputs required for tumour cell survival in the setting of targeted cancer therapies. These findings suggest that the addition of THZ1 to targeted cancer therapies is a promising broad-based strategy to hinder the emergence of drug-resistant cancer cell populations.

overall_design: RNA-seq in tumor cell lines treated with targeted therapies and/or transcriptional inhibitors

first: Maria

last: Rusan

first: Kapsok

first: Yvonne

first: Camilla

middle: L

last: Christensen

first: Brian

last: Abraham

first: Nicholas

last: Kwiatkowski

first: Kevin

last: Buczkowski

first: Bruno

last: Bockorny

first: Ting

last: Chen

first: Shuai

last: Rhee

first: Haikuo

first: Wankun

first: Hideki

last: Terai

first: Tiffany

last: Tavares

first: Tinghu

first: Tae

last: Kim

first: Sook-hee

last: Hong

first: Neermala

middle: P

last: Neupane

first: Michael

last: Silkes

first: Tenny

last: Mudianto

first: Li

last: Tan

first: Takeshi

last: Shimamura

first: Matthew

last: Meyerson

first: Hideo

last: Watanabe

first: Nathanael

middle: S

last: Gray

first: Kwok-Kin

last: Wong

first: Peter

last: Hammerman


title: Suppression of adaptive responses to targeted cancer therapy by transcriptional repression

first: Richard

last: Young


title: Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells

city: Leiden

first: Stefan

last: Semrau

state: Zuid-Holland

address: Einsteinweg 55

department: Physics

country: Netherlands

institute: Leiden University

summary: Gene expression heterogeneity in the pluripotent state of mouse embryonic stem cells (mESCs) has been increasingly well-characterized. In contrast, exit from pluripotency and lineage commitment have not been studied systematically at the single-cell level. Here we measured the gene expression dynamics of retinoic acid driven mESC differentiation using an unbiased single-cell transcriptomics approach. We found that the exit from pluripotency marks the start of a lineage bifurcation as well as a transient phase of susceptibility to lineage specifying signals. Our study revealed several transcriptional signatures of this phase, including a sharp increase of gene expression variability and a handover between two classes of transcription factors. In summary, we provide a comprehensive analysis of lineage commitment at the single cell level, a potential stepping stone to improved lineage control through timing of differentiation cues.

overall_design: Bulk and single-cell RNA-seq (SCRB-seq and SMART-seq) of mouse embryonic stem cells after different periods of continuous exposure to retinoic acid. Bulk RNA-seq of cell lines derived after retinoic exposure and after differentiation with retinoic acid and MEK inhibitor combined.

first: Alexander

last: van Oudenaarden


title: Type I interferon signaling attenuates regulatory T cell function in viral infection and in the tumor microenvironment

first: Craig

last: Martens

summary: Regulatory T cells (Tregs) play a cardinal role in the immune system by suppressing detrimental autoimmune responses, but their role in acute/chronic infectious diseases and in the tumor microenvironment remains unclear. We recently demonstrated that IFN-a/b receptor (IFNAR) signaling promotes Treg function in autoimmunity. Here, we dissected the functional role of IFNAR-signaling in Tregs using Treg-specific IFNAR deficient (IFNARfl/flxFoxp3YFP-Cre) mice in acute LCMV Armstrong, chronic LCMV Clone-13 infection, and in a transplantable colon adenocarcinoma model. In both viral and tumor models, IFNARfl/flxFoxp3YFP-Cre mice Tregs expressed enhanced Treg associated activation antigens. The enhanced activated phenotype was also seen when we compared the transcriptomes of IFNARfl/flxFoxp3YFP-Cre mice Tregs with the wild type (WT) Tregs by RNA-Seq on day 5 Armstrong and day 25-post Clone-13 infection. LCMV-specific CD8+ T cells and tumor infiltrating lymphocytes from IFNARfl/flxFoxp3YFP-Cre mice produced less antiviral and antitumor IFN-g and TNF-a. In the chronic infection model, the numbers of antiviral effector and memory CD8+ T cells were decreased in IFNARfl/flxFoxp3YFP-Cre mice and the effector CD4+ and CD8+ T cells exhibited a phenotype compatible with enhanced exhaustion. IFNARfl/flxFoxp3YFP-Cre mice cleared Armstrong infection normally, but had higher viral titers in sera, kidneys and lungs during chronic infection, and a higher tumor burden than the WT controls. Thus, type I IFN signaling in Tregs is context-dependent, resulting in enhanced suppressor function in some models of autoimmunity, but decreased suppressor function in acute/chronic viral infection and in the tumor microenvironment.

overall_design: mRNA from Treg cells from 4 WT and 4 IFNAR deficient mice were analyzed by RNA-seq using Illumina HiSeq 5 days post LCM Armstrong infection.

first: Arunakumar

last: Gangaplara

first: Eric

last: Dahlstrom

first: Amina

last: Metidji

first: Ameya

last: Gokhale

first: Deborah

last: Glass

first: Maria

last: Lopez-Ocasio

first: Rachel

last: Schmidt

first: Kishore

last: Kanakabandi

first: Stephen

last: Porcella

first: Ethan

middle: M

last: Shevach


title: Effect of reducing insulin signaling on third instar larval fat body gene expression in Drosophila melanogaster

city: Binghamton

first: Laura

middle: Palanker

last: Musselman

address: 4400 Vestal Parkway East

institute: Binghamton University

summary: We characterized insulin receptor (InR)-dependent gene expression in the Drosophila fat body using transgenic RNAi. Chronic knockdown of InR in the fat body was elicited via (r4-GAL4, UAS-InRi) and RNA-seq was used to identify potential target genes.

overall_design: Drosophila were reared on control (0.15 M sucrose) or high sugar (0.7 M sucrose) diets until the wandering third instar stage. Control (r4-GAL4 x w1118) offspring were compared with InRi (r4-GAL4 x UAS-InRi) using the VDRC's w1118 (#60000) or UAS-RNAi targeting InR (#992).  Fat bodies were isolated, and RNA was extracted to determine the effects of reduced insulin signaling on gene expression using Illumina RNA-seq.

first: Thomas

last: Baranski


title: Effect of increased insulin signaling on third instar larval fat body gene expression in Drosophila melanogaster

summary: We characterized constitutively active insulin receptor (InR)-dependent gene expression in the Drosophila fat body. Transient activation of InR was elicited via heat shock and RNA-seq was used to identify potential target genes.

overall_design: Drosophila were reared on control diets until the third instar stage. Control (hs-GAL4 x y1w1118) offspring were compared with InRCA (hs-GAL4 x UAS-InR.A1325D).  Fat bodies were isolated 6 hours after a heat shock, and RNA was extracted to determine the effects of transiently increased InR activation on gene expression using Illumina RNA-seq.


title: Transcriptional profiles of skeletal muscles in mice exposed to acute hypoxia

city: La Jolla

first: Andrew

middle: Douglas

last: McCulloch

address: 9500 Gilman Drive

department: Bioengineering

institute: UC San Diego

summary: To understand the underlying gene changes in in vivo muscles during acute hypoxic exposure, we studied the transcriptional profiles of in vivo skeletal muscles from mice exposed to 8% O2 for 0 hours, 2 hours, and 6 hours. For each condition, we extracted total RNA from fresh in vivo plantaris muscles for 3 biological replicates. The NGS data was acquired using paired-end 100bp by Illumina HiSeq 2000 with a depth around 100X. The quality control of raw data indicated excellent quality of sequencing data with quality scores in the range of 33-40 all over the reads. The analysis of differential expressed genes indicated quick genes responses in skeletal muscles in both 2 and 6 hours of hypoxia. The gene changes indicated a shift from genes associated with extracellular lumen in 2 hours of hypoxia to genes associated with the nuclear lumen in 6 hours of hypoxia. Signaling pathways such as PI3K/Akt signaling, mTOR signaling, MAPK signaling showed enriched gene responses. The KEGG-pathway based pathway-network analysis suggested the PI3K/Akt signaling pathway as a nodal pathway among the gene response-enriched pathways during acute hypoxia. Our Western blot experiments indicated a functional down-regulation of PI3K/Akt signaling by de-phosphorylation of Akt.

overall_design: Gene expressions in in vivo skeletal muscles exposed to 8% O2 for 2 hours and 6 hours

middle: D

first: Zhuohui

last: Gan


title: Type I interferon signaling attenuates Regulatory T cells function in LCMV infection

summary: Regulatory T cells (Tregs) play a cardinal role in the immune system by suppressing detrimental autoimmune responses, but their role in acute and chronic infectious diseases remains unclear. We recently demonstrated that IFN- receptor (IFNAR) signaling promotes Treg function in autoimmunity. To dissect the functional role of IFNAR-signaling in Tregs during acute and chronic viral infection, we infected Treg-specific IFNAR deficient (IFNARfl/flxFoxp3YFP-Cre) mice with LCMV Armstrong and Clone-13. In both models, IFNARfl/flxFoxp3YFP-Cre mice Tregs expressed enhanced expression of Treg associated activation antigens. The enhanced activated phenotype was also seen when we compared the transcriptomes of IFNARfl/flxFoxp3YFP-Cre and wild type (WT) Tregs by RNA-Seq on day 25-post Clone-13 infection. LCMV-specific CD8+ T cells from IFNARfl/flxFoxp3YFP-Cre mice produced less antiviral IFN and TNF in both acute and chronic LCMV. In the chronic model, the numbers of anti-viral effector and memory CD8+ T cells were decreased in IFNARfl/flxFoxp3YFP-Cre mice and the effector CD4+ and CD8+ T cells exhibited a phenotype compatible with enhanced exhaustion. IFNARfl/flxFoxp3YFP-Cre mice cleared Armstrong infection normally, but had higher viral titers in sera, kidneys and lungs than WT mice during chronic infection. Thus, type I IFN signaling in Tregs is context-dependent, resulting in enhanced suppressor function in some models of autoimmunity, but decreased suppressor function in acute and chronic viral infection.

overall_design: mRNA from Treg cells from 5 WT and 5 IFNAR deficient mice were analyzied by RNA-seq using Illumina HiSeq


title: Transcriptome analysis of human airway epithelium infected by Human Bocavirus 1

status: Public on Oct 22 2017

city: Kansas City

first: Jianming

last: Qiu

state: KS

address: 3901 rainbow blvd

department: Microbiology

institute: University of Kansas Medical Center

summary: Human Bocavirus 1(HBoV1), which belongs to the genus Bocaparvovirus of the family Parvoviridae, infects well differentiated human airway epithelium which is at mitotically quiescent state. To systematicaly investigate the interaction between HBoV1 and primary human airway epithelium cultured at an air-liquid interface (HAE-ALI), RNA-seq was applied to study the transcriptome profile of HAE-ALI infected by HBoV1.

overall_design: Primary human airway epithelial cells were cultured on collagen-coated, semipermeable membrane inserts of 0.33 cm2 and were polarized/differentiated at an ALI for 3-4 weeks. The well differentiated HAE-ALI cells were infected with HBoV1 at a multiplicity of infection (MOI) of 1,000 vgc/cell. At 7 days post infection, mock and HBoV1 infected-cell were collected and RNA samples were prepared using the miRNeasy Mini Kit by following the manufacturer’s instruction. HAE cells from two Transwells were used as one RNA sample, totally 6 RNA samples from HBoV1 infected HAE-ALI cultures and 6 RNA samples from mock-infected HAE-ALI cultures were performed for RNA isolation. All RNA samples were analyzed on an Agilent 2100 Bioanalyzer with an Agilent RNA 6000 Nano Kit to ensure an RNA Integrity Number (RIN) ≥ 8.0. Three RNA samples were chosen randomly from each group and used for RNA-seq.

first: Min

last: Xiong

first: Wei

last: Zou

first: Xuefeng

last: Deng


title: Analysis of genome-wide accessibility following acute deletion of Ring1b in mouse embryonic stem cells [ATAC-seq]

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

summary: Knockout of the PRC1 catalytic subunit Ring1b does not induce widespread accessibility increases at bivalent TSSs as measured by ATAC-seq. Instead, accessibility changes are enriched at enhancers.

overall_design: Examination of genomic accessibility using ATAC-seq in mouse embryonic stem (ES) cells expressing conditional knockout alleles of the PRC1 subunit Ring1b. For Ring1a-null;Ring1b-CreER (Ring1bflfl) conditional knockout cells, ATAC was performed 72 h after treatment with either ethanol (EtOH) or 0.8 uM 4-hydroxytamoxifen (Tam).

first: Courtney

first: Benjamin

middle: Z

last: Stanton

first: Katerina

last: Cermakova

first: Chiung-Ying

last: Chang

first: Erik

last: Miller

first: Jacob

middle: G

last: Kirkland

first: Wai

last: Ku

first: Vaclav

last: Veverka

first: Keji

last: Zhao

first: Gerald

last: Crabtree


title: Stress-induced accumulation of DNA N6-Methyladenine in prefrontal cortex

city: Atlanta

first: Bing

last: Yao

state: GA

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

summary: Chemical covalent modifications on the 5-carbon position of cytosine, such as 5- methylcytosine and 5-hydroxymethylcytosine, are a set of well-characterized epigenetic marks that shape transcriptional landscaping. Compiling evidence suggests central roles of cytosine modification dynamics in neuronal functions such as memory formation and stress response. N6-methyladenine (6mA) that previously described in bacteria has been recently found in higher eukaryotes, including worms, flies and mice. However, the precise roles and molecular mechanisms of 6mA in mammalian genome, particularly CNS, remain vague. Here we report that the global 6mA level is elevated in mice prefrontal cortex (PFC) upon restraint stress. The 6mA dynamics responding to stress is independent of Tet1 and Tet2 proteins, whose Drosophila ortholog serves as a 6mA demethylase. Genome-wide 6mA profiling in control and stressed PFC reveal that 6mA dynamic changes upon stress predominantly occur on intragenic introns and repetitive elements. Global transcriptome analyzes indicate a set of upregulated genes bearing elevated 6mA levels are highly enriched in neuronal pathways response to stress, suggesting a positive correlation of 6mA with transcription of these loci. In addition, 6mA dynamics in stress response could also influence transposon expression. Furthermore, 6mA is depleted in cortex enhancers, indicating their cis-regulatory roles in transcription. Motif identifications using 6mA dynamic regions provide putative transcription factors and epigenetic modulators binding sites with mechanistic hints. Taken together, our findings reveal dynamic 6mA changes in mice PFC in response to stress, and define its potential epigenetic roles in modulating gene and transposon expression.

overall_design: Examine the roles of 6mA in mice prefrontal cortex upon environmental stress


title: RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit [RNA-Seq]

city: Grenoble

first: Camille

last: Sayou

address: 17 avenue de Martyrs

department: BGE UA13

country: France

institute: CEA, IRIG

summary: Genome wide screens identified negative genetic interactions between several cofactors of the exosome nuclease complex and the Bre5-Ubp3 ubiquitin protease complex. RNA-binding was shown for Bre5 with enrichment for sites over exon 2 of spliced pre-mRNAs and close to poly(A) sites. An inducible splicing-reporter showed a requirement for Bre5 in efficient in vivo splicing and for normal RNAPII elongation, specifically on splicing-competent genes. A Bre5-Ubp3 sensitive site of RNAPII ubiquitination was mapped at Lys1246 at the entrance to the active site of the large subunit. Ubiquitinated RNAPII was depleted at the TSS but enriched at the 5’ end of exon 2 and upstream of poly(A) sites, similar to Bre5. Mutation of Lys1246 reduced RNAPII occupancy upstream of the poly(A) site, consistent with reduced pausing at a potential surveillance site, but increased RNAPII residence downstream of the poly(A) site. Strains expressing RNAPII with the Lys1246 mutation showed increased levels of unspliced but poly(A)+ RNA, indicating reduced cotranscriptional splicing efficiency. We propose that ubiquinitation of RNAPII is induced by RNA processing events and linked to transcriptional pausing, which is released by Bre5-Ubp3 associated with the nascent transcript.

overall_design: RNA-Seq of the S. cerevisiae transcriptome was conducted to compare the presence of unspliced introns in strains expressing Rpo21-HTP or Rpo21_K1246R-HTP.

first: Laura

last: Milligan

first: Alex

last: Tuck

first: Jane

middle: E

last: Reid

first: Ross

last: Alexander

first: Flavia

last: de Lima Alves

first: Juri

last: Rappsilber

first: Jean

last: Beggs

first: Gregorz

last: Kudla

first: David

last: Tollervey


title: Transcriptome analysis reveal the mechanism of Fungicidal of Thymol against Fusarium oxysporum f.sp. niveum

status: Public on Oct 21 2017

city: Nanjing

first: Xiangyang

last: Yu

state: Jiangsu

address: 50 Zhongling Road

institute: Jiangsu Academy of Agricultural Sciences

summary: Thymol (5-methyl-2-(1-methylethyl) phenol, PubChem CID: 6989) has been extensively reported to have antimicrobial activity against pathogenic microorganisms. In this study, the growth of F. oxysporum was significantly inhibited by thymol in vitro. The dry weight of F. oxysporum was decreased significantly. Thymol-induced cell membrane damage was observed at 24 hpi (hours post incubation). Therefore, the changes in the gene expression level of F. oxysporum after treatment with 80 μg/mL (average EC50 value) of thymol were analyzed using RNA-seq to reveal the underlying fungicidal mechanisms of thymol.

overall_design: F. oxysporum was cultured in PDB as a control, the F. oxysporum cultured in PDB with 80 μg/mL of thymol was the experiment group. Three biological replicates were performed.


title: Whole transcriptome analysis of iPSC-derived hepatic organoids cultures

city: Stanford

first: Ming

last: Zheng

address: Room L212, Lane Bldg

institute: Stanford University

summary: A heatmap, which focused upon 2458 genes that were involved in stem cell differentiation and liver development, was prepared to visualize the relative relationship between the transcriptomes of iPSCs, PHHs, human liver tissue and HO1. The dendrogram indicates that HO1 is more closely related to liver tissue than to PHHs; this is because cholangiocytes are present in HO1 and liver, but are absent (or rare) in PHHs. Examination of the genes within this heatmap indicated that there was a lack of expression of pluripotent genes in HO1; and that HO1 had an increased level of expression of cellular markers for liver lineages and liver development, which included mature hepatocytes, bile duct cells and NOTCH signaling components. A cluster analysis of 1510 genes indicates that there were major changes in the transcriptome after the cells that were dissociated from an HO1 were transferred from the growth medium into the differentiation medium. As with the HO1s, the gene expression profile of HO2s resembled that of PHHs and human liver. Of importance, the level of expression of mRNAs that are of importance for various human liver functions (ADH4, CYP3A4, TTR, GSRA1, TDO2, GSTA1 and FAH) were markedly increased in HO2s.

overall_design: Whole transcriptome analysis was performed on iPSCs, primary human hepatocytes (PHH), HO1 (primary hepatic organoids) and human liver tissue. For this analysis, over 100 organoids that were generated from a single donor were analyzed. Next, whole transcriptome analysis was performed to characterize HO2s (secondary organoids) and their relationship to iPSCs, PHHs and human liver tissue. This analysis utilized 1,000 HO2s that were prepared from a single donor.

first: Yuan

last: Guan


title: Substoichiometric ribose methylations in spliceosomal snRNAs

status: Public on Oct 20 2017

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: Sequencing-based profiling of ribose methylations is a new approach that allows for experiments adrressing dynamic changes on a large scale. Here, we apply such a method to spliceosomal snRNAs present in human whole cell RNA. Analysis of solid tissue samples confirmed all previously known sites and demonstrated close to full methylation at almost all sites. Methylation changes were revealed in biological experimental settings, using T cell activation as an example, and in the T cell leukemia model, Jurkat cells. Such changes could impact the dynamics of snRNA interactions during the spliceosome cycle and affect mRNA splicing efficiency and splicing patterns.

overall_design: 12 biological samples analysed in technical triplicates, in total 36 samples

first: Martin

last: Kongsbak-Wismann

first: Carsten

last: Geisler

first: Henrik

last: Nielsen


title: Post-transcriptional Gene Silencing Mediated by microRNAs is Controlled by Nucleoplasmic Sfpq [RNA-Seq]

city: Nice

first: Silvia

last: Bottini

address: 299, chemin de la ginestiere

summary: There is a growing body of evidence about the presence and the activity of the miRISC in the nucleus of mammalian cells. Here, we show by quantitative proteomic analysis that Ago2 interacts with nucleoplasmic Sfpq in a RNA-dependent fashion. By HITS-CLIP and transcriptomic analyses, we demonstrated that Sfpq directly controls the miRNA targeting of a subset of crucial miRNA-target mRNAs when it binds locally. Sfpq modulates miRNA targeting in both nucleoplasm and cytoplasm, indicating a nucleoplasmic imprinting of Sfpq-target mRNAs that influence miRNA targeting in both cellular compartments. Mechanistically, Sfpq binds to a sizeable set of long 3’UTR forming long aggregates to optimize miRNA position/recruitment to selected binding sites, as we show for Lin28A mRNA. These results extend the miRNA-mediated post-transcriptional gene silencing into the nucleoplasm and indicate that an unique Sfpq-dependent post-transcriptional strategy for controlling both nuclear and cytoplasmic gene expression takes place in cells during physio-pathological events.

overall_design: RNA-seq of P19 cells control and upon SFPQ knockdown both in triplicates

first: Nedra

last: Hamouda-Tekaya

first: Raphael

last: Mategot

first: Laure-Emmanuelle

last: Zaragosi

first: Stephane

last: Audebert

first: Valerie

last: Grandjean

first: Claire

last: Mauduit

first: Mohamed

last: Benahmed

first: Pascal

last: Barbry

first: Emanuela

last: Repetto

first: Michele

last: Trabucchi


title: Post-transcriptional Gene Silencing Mediated by microRNAs is Controlled by Nucleoplasmic Sfpq

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

overall_design: Refer to individual Series


title: Suppression of adaptive responses to targeted cancer therapy by transcriptional repression [ChIP-seq]

first: Richard

last: Young

overall_design: ChIP-Seq for enhancer-binding proteins in multiple tumor cell lines

first: Maria

last: Rusan

first: Kapsok

last: Li

first: Yvonne

first: Camilla

last: Christensen

first: Brian

last: Abraham

first: Nicholas

last: Kwiatkowski

first: Kevin

last: Buczkowski

first: Bruno

last: Bockorny

first: Ting

last: Chen

first: Shuai

last: Rhee

first: Haikuo

last: Zhang

first: Wankun

first: Hideki

last: Terai

first: Tiffany

last: Tavares

first: Tinghu

first: Tae

last: Kim

first: Sook-hee

last: Hong

first: Neermala

last: Neupane

first: Michael

last: Silkes

first: Tenny

last: Mudianto

first: Li

last: Tan

first: Takeshi

last: Shimamura

first: Matthew

last: Meyerson

first: Hideo

last: Watanabe

first: Nathanael

last: Gray

first: Kwok-Kin

last: Wong

first: Peter

last: Hammerman


title: RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit [CRAC]

first: Camille

last: Sayou

overall_design: RNA binding by Bre5 and Rpo21 was analysed by CRAC in S. cerevisiae. Bre5 full length protein carried a C-terminal HTP tag, in the wild-type background, in the absence of Ubp3 (ubp3∆), or in an rsp5-3 temperature sensitive strain. Bre5-HTP was analysed using a standard CRAC procedure (Granneman et al., 2009). Rpo21 full length protein also carried a C-terminal HTP tag, in the wild-type background or in the absence of Bre5 (bre5∆). To map the locations of RNAPII containing ubiquitinated Rpo21 we applied modification CRAC (mCRAC), including an affinity purification step to specifically enrich for ubiquitinated proteins using a MultiDsk construct (MD), comprised of five UBA domains from the yeast ubiquitin-binding protein Dsk2 fused to GST (Wilson et al., 2012). This procedure led to three samples: “GST-FT” represents the total Rpo21, “MD” represents the ubiquitinated Rpo21, “GST” represent the non-specific binding to a GST column. Rpo21-K1246-HTP was analysed using a standard CRAC procedure. All protein genes were tagged at their endogenous locus and were expressed under the control of their endogenous promoter. We have included duplicates samples and an untagged BY4741 negative control.

first: Laura

last: Milligan

first: Alex

last: Tuck

first: Jane

last: Reid

first: Ross

last: Alexander

first: Flavia

last: de Lima Alves

first: Juri

last: Rappsilber

first: Jean

last: Beggs

first: Gregorz

last: Kudla

first: David

last: Tollervey


title: CDK7 Inhibition Suppresses Melanoma Growth By Depleting A Super-enhancer Associated "Achilles" Lineage Cluster

first: Richard

last: Young


title: CDK7 Inhibition Suppresses Melanoma Growth By Depleting A Super-enhancer Associated "Achilles" Lineage Cluster [ChIP-Seq]

summary: Cutaneous malignant melanoma (CMM) lacks targeted therapies beyond the oft-circumvented BRAF inhibitors.  Part of the difficulty in treating melanomas has been attributed to a strong survival program controlled by melanocyte transcription factors such as MITF - a phenomenon first described in melanoma as “lineage dependency.”  Recently, a highly selective covalent CDK7 inhibitor (THZ1) has been shown to potently suppress the growth of various cancers through the depletion of master transcription-regulating oncogenes and the disruption of their attendant super-enhancers.  We now show that melanoma cells are highly sensitive to CDK7 inhibition and that a melanocyte “lineage cluster,” whose members are transcriptionally driven by super-enhancers, is also strongly suppressed by THZ1.  These results point to CDK7 inhibition as a viable strategy to deprive oncogenic transcription and suppress tumor growth in melanoma.

overall_design: ChIP-Seq for BRD4 and RNA Pol II in SK-MEL-5 melanoma cells

first: Philip

last: Eliades

first: Brian

last: Abraham

first: Camilla

last: Christensen

first: Nicholas

last: Kwiatkowski

first: Zhenyu

last: Ji

last: Miller

first: Benchun

last: Miao

first: Raj

last: Kumar

first: Michael

last: Taylor

first: Ching

middle: N

last: Njauw

first: Hensin

last: Tsao

first: Lars

last: Anders


title: RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit

first: Camille

last: Sayou


title: ChIP-seq from CD14-positive monocyte (ENCSR065SKV)

status: Public on Oct 18 2017

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
ChIP-seq

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


title: ChIP-seq from CD14-positive monocyte (ENCSR102GGG)