GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM3334225

Query DataSets for GSM3334225

Status

Public on Oct 11, 2018

Title

UB_RNASeq

Sample type

SRA

Source name

Ureteric epithelium

Organism

Mus musculus

Characteristics

tissue: Ureteric epithelium
cell type: Ureteric epithelium (manually dissected)
strain: C57BL/6
genotype: wild type
age: E11.5
chip antibody: n/a

Extracted molecule

total RNA

Extraction protocol

Libraries were prepared using SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech Laboratories)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

Cuffdiff_MM_UB_transcript_FPKM.tabular

Data processing

For ChIP-seq analysis, the replicate was concatenated and mapped using Bowtie2 at default setting.
ChIP-seq peaks were called using MACS14 against the input control data. The parameter set used in MACS14 was as follows: H3K4me3 (Band width 300, Pvalue cutoff 1e-05, the nearby regions to calculate dynamic lambda 1000-10000) and H3K27me3 (Band width 2900, Pvalue cutoff 1e-04 (mES and MM(Cited1)) or 1e-03 (UB), the nearby regions to calculate dynamic lambda 1000-20000).
Peaks were annotated with overlapping genes using AnnotateGenomicRegions ( https://sourceforge.net/projects/annotatelocus/files/webarchive/JSFversion/AnnotateGenomicRegions.war/download)
For RNA-seq analysis, all sequencing reads were mapped using Tophat at default setting.
Aligned RNA-seq reads were further analyzed using Cufflinks, Cuffmerge, and Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq: BED files with called peaks on sample records and peak annotation files on series record.
RNA-seq: text file with FPKM

Submission date

Aug 15, 2018

Last update date

Oct 11, 2018

Contact name

Masaki Nishikawa

E-mail(s)

masakiwestriver@gmail.com

Organization name

UCLA / VA

Lab

Yanagawa