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Sample GSM1381989 Query DataSets for GSM1381989
Status Public on Jul 14, 2014
Title EGR1
Sample type SRA
Source name overexpression of EGR1 in Embryonic stem cells; cells collected 5 days after transduction
Organism Homo sapiens
Characteristics cell type: ES-derived cells
cell line: H1
passage: 30-38
Growth protocol H1 cells were maintained on matrigel-coated plates in a regular TeSR1 media, supplemented with 4ng of human FGF2. For lenti-viral transductions, cells were washed with PBS, dissociated to a single cell suspension by incubating with Accutase (Invitorgen cat.#A1110501) for 5-7 minutes, collected, pelleted and resuspended in 1-2ml of mTeSR1 media. For one well of 6-well plate 0.68 x10^6 cells were mixed with concentrated viral media (MOI 1-5) in 1ml in the presence of polybrene (6ug/ml), plated on matrigel-coated plates and placed in the cell culture incubator for 12hr. After 12hr, attached cells were maintained in a basal TeSR1 media with hFGF-20ng, SCF-100ng and TPO-50ng. Submitted RNA samples are from cells collected as indicated in “title” for the sample. Non-transduced hESCs grown in the same culture conditions were used as a control.
Extracted molecule total RNA
Extraction protocol RNA isolation procedure was performed according to QIAGEN protocol for RNAeasy micro kit Cat# 74004
Samples were then prepared for sequencing using the Illumina TruSeq RNA Sample Preparation Kit v2 (RS-122-2001), according to the manufacturer's protocol
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 "
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files containing non-normalized "Expected Counts" and normalized "Transcripts Per Million" expression estimates calculated by RSEM.
Supplementary_files_format_and_content: normalized expression estimates
Supplementary_files_format_and_content: non-normalized abundance estimates
Submission date May 07, 2014
Last update date May 15, 2019
Contact name Scott Swanson
Organization name Morgridge Institute for Research
Lab Thomson
Street address 330 N. Orchard St
City Madison
State/province WI
ZIP/Postal code 53715
Country USA
Platform ID GPL16791
Series (1)
GSE57395 Direct Induction of Hematoendothelial Program in Human Pluripotent Stem Cells by Transcriptional Regulators
BioSample SAMN02767208
SRA SRX535113

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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