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Sample GSM871703 Query DataSets for GSM871703
Status Public on Dec 07, 2012
Title K77.5-WT
Sample type SRA
Source name Nkx2-1-iCre targeted eGFP+ cells
Organism Mus musculus
Characteristics strain: Swiss
genotype/variation: WT
developmental stage: E14.5
tissue: telencephalon
method: FACsorted cells
Treatment protocol FACsorting
Extracted molecule total RNA
Extraction protocol Trizol followed by RNeasy micro. RNA seq library is prepared for analysis according to the Illumina TruSeq protocol ( Briefly, 100 ng of Total RNA is purified using poly-T oligo-attached magnetic beads to end up with poly-A containing mRNA. The Poly-A tailed mRNA is fragmented and cDNA is synthesized using SuperScript II. cDNA fragments is end repaired, purified with AMPure XP beads, A-tailed using Klenow exo-enzyme in the presence of dATP. Illumina provided paired end adapters with index are ligated to the A-tailed cDNA fragments and purified using AMPure XP beads. The resulting adapter-modified cDNA fragments are enriched by PCR using Phusion polymerase as follow: 30 s at 98°C, 15 cycles of (10 s at 98°C, 30 s at 60°C, 30 s at 72°C), 5 min at 72°C. PCR products are purified using AMPure XP beads and eluted in 30 µl of resuspension buffer. One microliter is loaded on an Agilent Technologies 2100 Bioanalyzer using a DNA 1000 assay to determine the library concentration and to check for quality. Cluster generation was performed according to the Illumina TruSeq SR Cluster kit v2 (cBot) Reagents Preparation Guide ( Briefly, 6 RNA-seq libraries were pooled together to get a stock of 10 nM. One microliter of the 10 nM stock was denaturated with NaOH, diluted to 6.5 pM and hybridized onto the flowcell. The hybridized products are sequentially amplified, linearized and end-blocked according to the Illumina Single Read Multiplex Sequencing user guide. After hybridization of the sequencing primer, sequencing-by-synthesis was performed using the HiSeq 2000 with a 36-cycle protocol. The sequenced fragments were denaturated with NaOH using the HiSeq 2000 and the index-primer was hybridized onto the fragments. The index was sequenced with a 7-cycle protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing alignment: Sequence reads were mapped to the mus musculus reference genome (mm9) via TopHat v1.2.0. Only uniquely mapping reads were taken into account.
counts: HTSeq v0.5.3p3 was used to count the number of genes for annotated genes. HTSeq was used in the “union” mode, with gene annotations from Ensembl release 62, grouping exons together based on gene_name (i.e., MGI symbols for protein-coding genes).
differential expression: normalization of gene expression levels and differential gene expression between WT and KO was calculated with DESeq v1.2.2.
Genome Build:
K77.5-WT-ACAGTG.counts.txt: mm9
Submission date Feb 07, 2012
Last update date May 15, 2019
Contact name Bram Van de Sande
Phone +32 16 33 01 42
Organization name KU Leuven
Department Center for Human Genetics
Lab Laboratory for Computational Biology
Street address Herestraat 49
City Leuven
ZIP/Postal code 3000
Country Belgium
Platform ID GPL13112
Series (1)
GSE35616 Sip1 in cortical interneuron migration
SRA SRX118796
BioSample SAMN00783735

Supplementary file Size Download File type/resource
GSM871703_K77.5-WT-ACAGTG.counts.txt.gz 131.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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