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| Status |
Public on Apr 29, 2013 |
| Title |
10ng_TR1 |
| Sample type |
SRA |
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| Source name |
embryoid body
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| Organism |
Mus musculus |
| Characteristics |
tissue: embryo
developmental stage: day 4 of differentiation
treatment: addition of Activin A (3ng/mL), mRNA amount 10ng; Technical replicate 1
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| Treatment protocol |
At day2 of differentiation, embryoid bodies were dispersed and treated with either Activin A or SB-431542 compound for two days.
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| Growth protocol |
Differentiating ESCs were grown in serum free conditions.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Day 4 embroid bodies treated with either Activin A or SB-431542 compound were harvest and total RNA was extracted for each sample. Later mRNA was isolated from each sample and single stranded cDNA was prepared. Sequencing libraries were generated by using our DP-seq strategy which involved generation of the amplicon library from defined heptamer primers based amplification. Std. RNA-seq libraries were prepared as described by Mortazavi et al. (2008). SMARTseq libraries were prepared as described by Ramsköld et al. 2012. 13 cycles of uniform cDNA amplifications were performed and the amplified libraries were verified on high sensitivity Bioanalyzer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava1.4 - SFM, SB, AA3, AA15, AA15_2,AA100,SFM_2
Illumina Casava1.7 - Ribo_primerset2, Ribo_primerset3
Illumina Casava1.8 - all rest of the samples
Sequence reads obtained from Illumina Genome Analyzer Iix were trimmed of first 2 and last 2 bases and mapped to mus musculus REFSEQ database using in-house mapping code allowing upto 2 mismatches
Sequence reads obtained from Illumina HiSEQ2000 were trimmed of first 14 bps (except for 10pg_TR2, 1pg_TR1 and 1pg_TR2) and next 32 bps were used for mapping with mus musculus REFSEQ database using in-house mapping code allowing upto 2 mismatches
Sequence reads obtained from Illumina HiSEQ2000 were trimmed of first 7 bps for 10pg_TR2, 1pg_TR1 and 1pg_TR2 and next 32 bps were used for mapping with mus musculus REFSEQ database using in-house mapping code allowing upto 2 mismatches
Genome_build: mus musculus REFSEQ database of RNA
Supplementary_files_format_and_content: tab-delimited text files include REFSEQ gene id and Unique Reads
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| Submission date |
Mar 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
vipul bhargava |
| E-mail(s) |
vipul.bhargava@gmail.com
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| Phone |
6198769520
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| Organization name |
ucsd
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| Street address |
9500 gilman drive
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| City |
la jolla |
| State/province |
California |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE45474 |
Quantitative Mammalian Transcriptomics using Designed Primer-based Amplification |
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| Relations |
| SRA |
SRX254910 |
| BioSample |
SAMN01990939 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1105131_v11_gene_copy.txt.gz |
122.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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