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| Status |
Public on Dec 04, 2012 |
| Title |
rat_ts_3seq_rep1 |
| Sample type |
SRA |
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| Source name |
Trophoblast stem cells
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: HSD
cell type: Trophoblast stem cells
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| 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). Rat TSCs were cultured as previously (Asanoma et al, Developmental Biology 2011)
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
mRNA
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| Data processing |
Basecalls performed using CASAVA version 1.5
ChIP-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 (sam_map.pl from Unipeak), and transcription peaks were called using default settings.
Peaks (chromosomal coordinates) were associated with Ensembl (e67) gene database for mouse and rat, and multiple peaks for each gene were pooled.
Genome_build: mm9
Supplementary_files_format_and_content: txt files contain pooled gene x raw tag count
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| Submission date |
Nov 09, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Edward Chuong |
| E-mail(s) |
edward.chuong@colorado.edu
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| Organization name |
University of Colorado Boulder
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| Department |
BioFrontiers
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| Lab |
Chuong
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| Street address |
596 UCB
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| City |
Boulder |
| ZIP/Postal code |
80304 |
| Country |
USA |
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| Platform ID |
GPL10669 |
| Series (1) |
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| Relations |
| SRA |
SRX204159 |
| BioSample |
SAMN01805512 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1035405_r_ts_3seq_counts.txt.gz |
290.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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