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Sample GSM1223563 Query DataSets for GSM1223563
Status Public on May 29, 2014
Title mouse_tgc_3seq_rep1
Sample type SRA
Source name Trophoblast giant cells - cultured
Organism Mus musculus
Characteristics strain: 129/Sv
cell type: cultured trophoblast giant cells
Treatment protocol TSCs were differentiated into trophoblast giant cells (TGCs) by using differentiation media, which consisted of TS media without FGF4, Activin, and Heparin, with the addition of retinoic acid dissolved in ethanol to the media to a final concentration of 5 μM. TSCs were differentiated for five days, replacing media every other day, before harvesting.
Growth protocol Mouse TSCs were obtained from Dr. Janet Rossant, Hospital for Sick Children, (Toronto, Canada) and maintained in DMEM/F12 with 15 mM Hepes, 20% FBS, 2 mM glutamine, 100 ug/ml streptomycin, 1 mM sodium pyruvate, 100 uM BME, supplemented with Activin, FGF4, and Heparin following (Erlebacher et al, Developmental Biology 2004).
Extracted molecule polyA RNA
Extraction protocol mRNA was extracted directly from cell lysates using Dynabeads Oligo (dT)25 (Invitrogen).
500 ng of mRNA was then used to prepare 3’ RNA-Seq libraries as previously described (Beck et al, PLOS One 2010). Briefly, mRNA was heat sheared for 7 minutes to produce an average fragment size range of 300-500 bp, then used to generate cDNA libraries using a custom oligo dT primer containing Illumina-compatible adapter sequence. cDNA fragments were end-repaired and ligated to standard Illumina adapters. Size-selection was performed using E-gel SizeSelect agarose gels (Invitrogen), products were PCR amplified for 15 cycles, and purified using Ampure XP beads. Library quality was assessed using Bioanalyzer and Qubit, and sequenced on the Genome Analyzer IIx.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Description Cell culture 3' RNA-Seq
Data processing Basecalls performed using CASAVA version 1.5
3' RNA-seq reads were aligned to mm9 or rn4 using Bowtie 0.12.7 with the settings --best --strata -k 10 -S --chunkmbs 190
Using Unipeak v1.0, Bowtie alignments were filtered by posterior probability ( from Unipeak), and transcription peaks were called using default settings.
Peaks (chromosomal coordinates) were associated with Ensembl (e67) gene database for mouse and multiple peaks for each gene were pooled.
Read counts were normalized across libraries using DESeq
genome build: = mm9
supplementary files format and content: txt files contain pooled gene x normalized tag count
Submission date Sep 03, 2013
Last update date May 15, 2019
Contact name Roberta L Hannibal
Organization name Stanford University
Department Genetics
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platform ID GPL11002
Series (2)
GSE50561 Trophoblast giant cell underrepresentation (sequencing)
GSE50585 Trophoblast giant cell underrepresentation
Reanalyzed by GSE80797
BioSample SAMN02344594
SRA SRX344649

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

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