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E-GEOD-19090 GSE19090 transcription profiling by array Homo sapiens

Exon arrays of ENCODE tier 1, tier 2 and tier 3 cell types

·Released Nov. 19, 2009 ·Updated May 2, 2014
174
Samples
174
Assays
1
Array Platforms
1
References
Description

At cell harvest, a subset of cells was stored at -20oC in RNALater. Total RNA from 5 X 106 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent). Approximately 3ug of total RNA for each cell type was sent to the Center for Array Technology (CAT) for labeling and hybridization to Affymetrix Human Exon 1.0 ST arrays. Briefly, a Whole Transcript Sense Target Labeling Assay (Affymetrix) was used by the CAT to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays. Hybridizations were carried out according the manufacturers protocol. Intensity files from the scanned exon arrays were sent to our lab for analysis at the exon level (Affymetrix ExACT 1.2.1 software). Samples were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized. For data usage terms and conditions, please refer to

References
Sequencing newly replicated DNA reveals widespread plasticity in human replication timing.
Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA
PMID: 19966280
Array Platforms
A-AFFY-143
Affymetrix GeneChip Human Exon 1.0 ST Array version 1, [HuEx-1_0-st-v1](174 items)
Sample Attributes
BioSourceProvider
ATCC;CCl-185, ATCC;CCL-2.2, ATCC;CCL-240, ATCC;CCL-243, ATCC;CCL-247, ATCC;CRL-146, ATCC;CRL-1573, ATCC;CRL-1740, ATCC;CRL-1973, ATCC;CRL-2268, ATCC;CRL-2522, ATCC;HB-8065, ATCC;HTB-10, ATCC;HTB-11, ATCC;HTB-169, ATCC;HTB-22, ATCC;HTB-37, ATCC;TIB-152, BresaGen;hESBGN.02, Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12864, Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12865, Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12866, Coriell;AG04449, Coriell;AG04450, Coriell;AG09309, Coriell;AG09319, Coriell;AG10803, Coriell;GM06990, Coriell;GM12878, DMSZ;NB4, Dr.Torok-Storb,FHCRC;HFF, Dr.Torok-Storb,FHCRC;HFF-Myc, DSMZ;ACC-392, FHCRC;HEIMFELD, Lonza;CC-2501, Lonza;CC-2505,CC-2505T225, Lonza;CC-2509, Lonza;CC-2511,CC-2511T225, Lonza;CC-2512, Lonza;CC-2517, Lonza;CC-2530,CC-3162, Lonza;CC-2540,CC3170, Lonza;CC-2543,CC-3202, Lonza;CC-2547, Lonza;CC-2553,CC-2553T225, Lonza;CC-2554, Lonza;CC-2555, Lonza;CC-2556, Lonza;CC-2561, Lonza;CC-2565, Lonza;CC-2580, Lonza;CC-2810,CC-2810T75, Lonza;CC-2811,CC-2811T75, Lonza;CC-2812,CC-2812T25, Lonza;CC-2813,CC-2813T75, Lonza;CC-2814, CC-2814T25, Lonza;CC-2815,CC-2815T75, Lonza;CC-3150, Lonza;CC-7014,CC-7014T75, None;(primary), RaskindUW;Raskind, SBIGeM, Dr.Carl Mann, ScienCell;1000, ScienCell;1100, ScienCell;1200, ScienCell;1310, Sciencell;1810, Sciencell;1820, ScienCell;1830, ScienCell;2620, ScienCell;2700, ScienCell;3120, ScienCell;3300, ScienCell;4000, ScienCell;6200, ScienCell;6300, ScienCell;6320, ScienCell;6540, ScienCell;6560, ScienCell;6570, ScienCell;6580, ScienCell;7100, ScienCell;7130, ScienCell;7409, ScienCell;7630, WiCell;WA07(H7)
cell line
GM12864, GM12865, NTERA-2 cl.D1, PrEC, WERI-Rb
cell type
acute promyelocytic leukemia cell line, Adult human abdominal skin fibroblasts, Adult Human Dermal Microvascular Endothelial Cells, Dermal-Derived., Adult human gum tissue fibroblasts, Adult human toe fibroblast, Adult Normal Human Dermal Fibroblasts, adult normal human epidermal keratinocytes, B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment: EBV transformed, cervical carcinoma, chronic myeloid leukemia, colorectal adenocarcinoma, colorectal carcinoma, embryonic kidney, Embryonic Lung Fibroblast Cells, hTERT, GFP-RAF-ER, Embryonic Lung Fibroblast Cells, hTERT, GFP-RAF-ER, treated with Tamoxifen, epithelial cell line derived from a lung carcinoma tissue, Fetal buttock/thigh fibroblast, Fetal lung fibroblast, flow sorted CD14+ primary cells, 32ys,Caucasian female,donor:RO 01746, Human Acute Megakaryocytic Leukemia Cells, Human Amniotic Epithelial Cells, Human astrocytes, cerebellar, Human astrocytes, spinal cord, Human Astrocytes-hippocampal, Human Brain Microvascular Endothelial Cells, Human Brain Vascular Pericytes, Human Brain Vascular Smooth Muscle Cells, Human Cardiac Fibroblasts, Human Cardiac Fibroblasts-Adult Atrial, Human Cardiac Myocytes, Human Choroid Plexus Epithelial Cells, Human Conjunctival Fibroblast, human embryonic stem cell (hESC) BG02, Human Esophageal Epithelial Cells, Human Foreskin Fibroblast, Human Foreskin Fibroblast Cells Expressing Canine cMyc, human gingaval fibroblast, Human Iris Pigment Epithelial Cells, human lymphoblastoid cell line derived from peripheral blood (male), Human Mammary Epithelial Cells, human mammary epithelial cells, Human Mammary Fibroblast, Human neuroblastoma, Human Non-Pigment Ciliary Epithelial Cells, human promyelocytic leukemia cells, Human Prostate Epithelial Cell line, Human Pulmonary Artery Endothelial Cells, Human Pulmonary Artery Fibroblasts, Human Pulmonary Fibroblasts, human renal cortical epithelial cells, human renal epithelial cells, Human Renal Glomerular Endothelial Cells, Human Retinal Pigment Epithelial Cells, Human skeletal muscle cells, human skeletal muscle cells, Human Umbilical Vein Endothelial Cell, Human Villous Mesenchymal Fibroblast Cells, liver carcinoma, lymphoblastoid, Malignant pluripotent embryonal carcinoma, NTERA-2 cl.D1 (PMID: 6694356), mammary gland, adenocarcinoma, Neonatal Human Dermal Fibroblasts, neuroblastoma cell line differentiated w/ retinoic acid, Neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, Normal Adult Human Blood Microvascular Endothelial Cells, Dermal-Derived, Normal Human Aortic Adventitial Fibroblast Cells, Normal Human Astrocytes, Normal Human Blood Microvascular Endothelial Cells, Lung-Derived, Normal Human Bronchial Epithelial Cells w/RA, Normal Human Lung Fibroblasts, Normal Human Lymphatic Microvascular Endothelial Cells, Lung-Derived, Normal Human Periodontal Ligament Fibroblast Cells, Normal Human Skeletal Muscle Myoblasts, Normal Human Skeletal Muscle Myoblasts, differentiated, Normal Neonatal Human Blood Microvascular Endothelial Cells, Dermal-Derived, Normal Neonatal Human Lymphatic Microvascular Endothelial Cells, Dermal-Derived, Normal Neonatal Human Microvascular Endothelial Cells (single Donnor), Dermal-Derived, pancreatic carcinoma, primary human Th1 T cells, primary human Th2 T cells, prostate adenocarcinoma, Renal Proximal Tubule Epithelial Cells, retinoblastoma (PMID: 844036), skin fibroblast, small airway epithelial cells, T lymphoblastoid cell line derived from an acute T cell leukemia, umbilical vein endothelial cells, Undifferentiated human embryonic stem cells
Organism
Homo sapiens
term
BTO:0000007, BTO:0000018, BTO:0000059, BTO:0000093, BTO:0000099, BTO:0000161, BTO:0000195, BTO:0000256, BTO:0000304, BTO:0000375, BTO:0000519, BTO:0000559, BTO:0000568, BTO:0000664, BTO:0000738, BTO:0000876, BTO:0000932, BTO:0000946, BTO:0001141, BTO:0001178, BTO:0001255, BTO:0001678, BTO:0001679, BTO:0001760, BTO:0001801, BTO:0001948, BTO:0001949, BTO:0002021, BTO:0002022, BTO:0002026, BTO:0002062, BTO:0002178, BTO:0002245, BTO:0002254, BTO:0002372, BTO:0002398, BTO:0002441, BTO:0002488, BTO:0002489, CL:0000007
Experiment Info
Accession
E-GEOD-19090
GEO ID
GSE19090
Type
transcription profiling by array
Organism
Homo sapiens
Released
Nov. 19, 2009
Updated
May 2, 2014
Submitter
J A Stamatoyannopoulos、 UCSC ENCODE DCC
Analysis Services
Analysis Services

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