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Sample GSM4125648

Query DataSets for GSM4125648

Status

Public on Mar 31, 2020

Title

whole_brain_K2_70

Sample type

SRA

Source name

E14.5_brain

Organism

Mus musculus

Characteristics

tissue: whole E14.5 brain
genotype/variation: Kansl2 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_kansl2_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