 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 30, 2017 |
| Title |
Csnk1e knockout mouse #3 : CB-4_L001 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Csnk1e knockout
brain area: Striatum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Csnk1e KO and WT mice at about 50 days of age were live-decaptitated for brain dissections. As mentioned before, 2.5mm strialtal punches (left and right hemispheres) were pooled per mouse, and collected tissue was immediately places into RNAlater (QIAGEN) for 48 hours. After incubation, RNA was extracted via miRNeasy Mini Kit and quality was assessed by Bioanalyzer analysis.
RNA that was deemed high quality was send to the University of Chicago Genomics Core Facility for cDNA library preparation. Libraries were prepared according to Illumina's detailed instructions accompanying the TruSeq® Stranded mRNA LT Kit (oligo-dT; 50bp single-end reads; Part# RS-122-2101). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
sample run across L001 & L0002 on flow cell1 and flow cell2
CB-4_L001
|
| Data processing |
Samples were run across four lanes (L001, L002, L001_2, L002_2) and reads for each sample were generated via the Illumina HiSeq 2500 (~10,000,000 reads per replicate, totalling ~40,000,000 per sample)
Fastq files are quality checked via FastQC (v0.10.1) and possessed Phred quality scores > 30 (i.e. less than 0.1% sequencing error)
Fastq files were utilized in TopHat (v2.0.0) to align reads to the reference genome (mm10; UCSC Genome Browser).
We computed the read counts per gene using the HTSeq (v0.6.1p1) Python package and edgeR (v2.14), a Bioconductor package for differential gene expression analysis that models read counts using a negative binomial distribution to account for variability in the number of reads via generalized linear models
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: HTseq output for each sample is in the form of a TXT (.txt) file that consists of a list of genes along side respective read counts.
|
| |
|
| Submission date |
Feb 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Lisa Goldberg |
| E-mail(s) |
lisagold@bu.edu
|
| Phone |
8605398638
|
| Organization name |
Boston University School of Medicine
|
| Street address |
72 E Concord St, R604
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE95141 |
RNA sequencing of striatum tissue from naive Csnk1e knockout mice and wild-type mice |
|
| Relations |
| BioSample |
SAMN06352552 |
| SRA |
SRX2580949 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2497600_htseq_CB-4_L001.txt.gz |
94.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
