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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 24, 2019 |
| Title |
Mouse placenta RNAseq CB E17 |
| Sample type |
SRA |
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| Source name |
mouse embryonic day 17.5 placental tissue
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| Organism |
Mus musculus |
| Characteristics |
genetic background: CAST/EiJ mother x C57BL/6 father
developmental stage: E17.5
tissue: placenta
Sex: Female
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| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA-seq libraries were made for F1 female placenta total RNA from AKRxPWD E17.5, PWDxAKR E17.5, B6xCAST E17.5, CASTxB6 E17.5, B6xCAST E13.5 and CASTxB6 E13.5 (mother comes first) crosses, using Illumina TruSeq RNA Sample Prep Kit (Illumina Inc., CA) with 4 µg of total mRNA input . The six mRNA-seq libraries were pooled and sequenced for three 51bp lanes on Illumina HiSeq2000 machine (Illumina Inc., CA). Image analysis and base calling were performed by the Illumina instrument software (Illumina pipeline CASAVA v1.7).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Illumina mRNA-seq
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| Data processing |
Illumina short reads were mapped to the mouse reference genome (UCSC mm9) using TopHat program with a maximum of 3 mismatches. Only uniquely mapped reads were used for allele-specific expression quantification. On average, 84% of the reads were uniquely mapped to the mouse genome. AKR-PWD and B6-CAST SNP information is obtained from Sanger mouse SNP database.
Genome Build:
mouse153_CB_E17_SNP_counts.txt: UCSC mm9
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| Submission date |
Mar 13, 2012 |
| Last update date |
May 24, 2019 |
| Contact name |
Andrew Clark |
| E-mail(s) |
ac347@cornell.edu
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| Organization name |
Cornell University
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| Street address |
227 Biotech Building
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| City |
Ithaca |
| ZIP/Postal code |
14853 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE36463 |
Profiling of differential allelic expression in mouse placental tissues from two reciprocal crosses at embryonic day 13.5 and 17.5. |
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| Relations |
| SRA |
SRX129171 |
| BioSample |
SAMN00811155 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM894312_mouse153_CB_E17_SNP_counts.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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