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Sample GSM4125651 Query DataSets for GSM4125651
Status Public on Mar 31, 2020
Title whole_brain_K3_149
Sample type SRA
 
Source name E14.5_brain
Organism Mus musculus
Characteristics tissue: whole E14.5 brain
genotype/variation: Kansl3 nKO
Treatment protocol FA treatment (FA were conjugated with BSA before application): 200 μM C14:0, 200 μM C16:0, 20 μM C20:0 and 10 μM C24:0. Vehicle: ethanol + BSA.
Growth protocol pericytes were extracted from the adult brain and maintained in Pericyte medium (ScienCell 1201) with the appropriate growth factors
Extracted molecule total RNA
Extraction protocol RNA from cultured pericytes, whole E14.5 brains and from neural cells was isolated using the Qiagen mini kit (#74104), while RNA from pericytes, endothelial cells and microglia was extracted using the Qiagen miRNeasy Micro kit (#1071023).
Libraries for RNA-seq of cultured pericytes, whole E14.5 brains and the neural population were prepared using the Illumina TruSeq library preparation kit. For pericytes, endothelial cells and microglia, cDNA was prepared from isolated RNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech 634891). Libraries were prepared using the Nextera XT DNA library preparation kit (Illumina FC-131-1096) and sequenced on the HiSeq Hiseq 3000 or NextSeq 500.
ChIP and library preparation for IP DNA was undertaken using the RELACS protocol (Arrigoni et al. 2018 Communications Biology)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description whole_brain_geneCounts.txt
whole_brain_kansl3_differential_genes.txt
Data processing RNA-seq: Raw sequencing data controlled for quality, trimmed and mapped to the reference mm10 genome using STAR (Dobin et al., 2013).
RNA-seq: The identity of reads was identified through FeatureCount (Liao et al., 2014).
RNA-seq: Differentially expressed genes were identified using DESeq2 (Love et al., 2014).
ChIP seq: Raw sequencing data controlled for quality, trimmed and mapped to the reference mm10 genome using Bowtie2 (Langmead B et al., 2012).
ChIP-seq: PCR duplicates were removed using sambamba (Tarasov et al., 2015)
ChIP-seq: coverage of ChIP and input was calculated and compared using deeptools bamCoverage and bamCompare (Ramirez et al., 2016)
Genome_build: mm10
 
Submission date Oct 16, 2019
Last update date Mar 31, 2020
Contact name Asifa Akhtar
E-mail(s) akhtarlab_data@ie-freiburg.mpg.de
Organization name Max Planck Institute of Immunobiology and Epigenetics
Department Chromatin Regulation
Lab Akhtar Lab
Street address Stuebeweg 51
City Freiburg
ZIP/Postal code 79108
Country Germany
 
Platform ID GPL19057
Series (1)
GSE138981 Analysis of NSL knockout brains
Relations
BioSample SAMN13041620
SRA SRX7007276

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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