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Sample GSM1511607 Query DataSets for GSM1511607
Status Public on Jun 03, 2015
Title Halr1_RNA-seq_JR735
Sample type SRA
Source name Halr1_RNA-seq_WT_Adult
Organism Mus musculus
Characteristics genotype/variation: WT
litternumber_id: linc-HoxA1_290-4
lncrna previous name: linc-HoxA1
Sex: male
timepoint: Adult
litter: NA
tissue: whole brain
Extracted molecule polyA RNA
Extraction protocol E14.5 whole brains were harvested and homogenized in TRIzol. Adult brains were harvested immediately after euthanasia, snap frozen in liquid nitrogen, and stored at -80C. These brains were pulverized in liquid nitrogen and homogenized in TRIzol.
Standard illumina protocols were used to make libraries (TruSeq RNA Sample Preparation Kit v2)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Casava 1.8.2 was used to call bases
Reads were aligned to mm10 using tophat2 (--no-coverage-search --max-multihits 10 -p 8)
Bams were quantified using cuffquant and a modified verson of the GENCODE M2 transcriptome (--no-update-check -p 8)
Differential analysis was performed using cuffdiff2 (-p 8)
Genome_build: mm10
processed data files format and content: the DiffTable output from cummeRbund, or essentially a tab-delimited file with all of the expression values and differential expression test statistics as called by cuffdiff for each gene in the transcriptome for each wt-v-ko comparison.
Submission date Sep 24, 2014
Last update date May 15, 2019
Contact name Abbie Groff
Organization name Harvard University
Department Stem Cell and Regenerative Biology;
Lab John Rinn
Street address 7 Divinity Ave
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
Platform ID GPL17021
Series (1)
GSE61716 Transcriptional perturbations by long noncoding RNAs with distinct spatio-temporal expression in the mammalian brain
BioSample SAMN03077720
SRA SRX709094

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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