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Series GSE76495 Query DataSets for GSE76495
Status Public on Oct 25, 2016
Title Multiparameter functional diversity of human C2H2 zinc finger proteins [RNA-Seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2 arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. We have determined the binding sites and motifs of 119 C2H2 zinc finger proteins and the expression pattern of 80 cell lines overexpressing C2H2 zinc finger proteins in order to study the role of C2H2 zinc finger proteins in gene regulation.
 
Overall design We expressed GFP-tagged C2H2-ZF proteins in stable transgenic HEK293 cells. Total RNA was isolated using Trizol and sequencing libraries were constructed using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold or TruSeq RNA Library Preparation Kit v2.
 
Contributor(s) Schmitges FW, Najafabadi HS, Radovani E, Greenblatt J, Hughes TR
Citation(s) 27852650
Submission date Jan 04, 2016
Last update date May 15, 2019
Contact name Hamed S Najafabadi
Organization name McGill University
Department Human Genetics
Lab Computational and Statistical Genomics Lab
Street address 740 Dr. Penfield Avenue, Room 7202
City Montreal
State/province QC
ZIP/Postal code H3A 0G1
Country Canada
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (92)
GSM2026902 RNA-seq data from HEK293 cell lines overexpressing GFP-tagged CTCF [CTCF_rep1]
GSM2026903 RNA-seq data from HEK293 cell lines overexpressing GFP-tagged EGR2 [EGR2_rep1]
GSM2026904 RNA-seq data from HEK293 cell lines overexpressing GFP-tagged EGR3 [EGR3_rep1]
This SubSeries is part of SuperSeries:
GSE76496 Multiparameter functional diversity of human C2H2 zinc finger proteins
Relations
BioProject PRJNA307572
SRA SRP068023

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MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE76495_OE.vsd_normalized.log2.txt.gz 6.6 Mb (ftp)(http) TXT
GSE76495_RAW.tar 20.3 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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