|
| Status |
Public on Jul 08, 2010 |
| Title |
POA_C57BL/6J_RNASeq_techrep1 |
| Sample type |
SRA |
| |
|
| Source name |
adult (5 week old) preoptic area
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
developmental stage: adult
age: 5 weeks old
tissue: brain
brain region: preoptic area
data type: transcriptome single nucleotide polymorphisms read counts
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sample isolation protocol: Whole embryonic day 15 brain tissue or adult (5 week old) medial prefrontal cortex or preoptic area was microdissected and RNA was isolated in Trizol, Dnase treated, and purified with Qiagen Rneasy MicroKit. For E15 brain samples, RNA was pooled from 4-5 different individuals for each sample. For adult mPFC and POA samples, RNA was pooled from 8-10 individuals per sample. RNA purity and quality was measured on an Agilant bioanalyzer and only samples with an RNA integrity score >9 were included. RNA was fragmented and converted to cDNA with random hexamer primers according to the Illumina RNA-Seq protocol. Size selection was done at 200+- 25 bp.
RNA-seq was performed accoring to the Illumina RNA-Seq protocol and cluster station reactions and sequencing was performed accoring to the Illumina sequencing kit protocols for 36 sequencing cycles. Each RNA sample was subject to 2 or more technical replicates and read data for each replicate was summed to generate the final processed dataset.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
poly A purified RNA from embryonic and adult brain converted to cDNA
mm9 UCSC annotated transcriptome
|
| Data processing |
Sequence data (reads were trimmed to 32 bases for analysis) was aligned using NovoAlign to the UCSC annotated mouse transcriptome (mm9) and mouse genome (mm9) and to the functional RNA database.
A reference table of CAST and C57 SNP sites was generated relative to the annotated reference transcriptome and genome for genes expressed in the E15 brain and adult mPFC and POA using the CastEiJ and C57BL/6J sequence data (E15 brain, POA, and mPFC). In cases where reads disagreed with the base call at a given SNP position, only SNP sites with a consensus of >80% for the base call at the SNP site were included in the final SNP reference table. Importantly, the base calls were confirmed by both parental strains. Transcript UCSC IDs (transcriptome alignment) or genome positions (genomic alignment) were recorded for each SNP containing read alignment, for example: uc007aeu.1_1263 (UCSC transcript ID_SNP base position). The SNP position was recorded relative to the first base of the transcript, or the base position relative to the start of the chromosome was recorded in the case of genomic alignments. Base calls at SNP sites for CAST and C57 samples relative to the annotated mouse transcriptome, genome, or fRNAdb were assembled into a CAST/C57 SNP Reference Table (see all tables labeled with "_SNP_calls.txt") and these SNP sites were used to assess allele-specific expression in the F1 hybrids. RNA Seq data from initial (F1i) and reciprocal (F1r) crosses of F1 hybrid mice was used to measure maternal and paternall allele specific expression at each SNP site. In the manuscripts, SNP site calls were further refined by requiring a minimum of 10 reads per SNP site for both the F1i and F1r crosses in the F1 hybrid datasets, however all SNP calls are presented in the raw processed files here.
Processed data file: POA_SNP_calls.txt
Processed data file(s) linked as supplementary files on Series GSE22131.
|
| |
|
| Submission date |
Jul 07, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Catherine Dulac |
| E-mail(s) |
dulac@fas.harvard.edu
|
| Organization name |
Harvard University
|
| Department |
Molecular and Cellular Biology
|
| Street address |
BL4017 16 Divinity Ave
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE22131 |
High resolution analysis of genomic imprinting in the embryonic and adult mouse brain AND Sex-specific imprinting in the mouse brain |
|
| Relations |
| SRA |
SRX023091 |
| BioSample |
SAMN00016871 |
