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Sample GSM4472170

Query DataSets for GSM4472170

Status

Public on Apr 11, 2020

Title

CT40 WT Biological Replicate 3

Sample type

SRA

Source name

Fetal Kidney

Organism

Mus musculus

Characteristics

strain: C57BL/6
developmental stage: E19 + 16 HRS
tissue: kidney

Extracted molecule

total RNA

Extraction protocol

Fetal kidneys were extracted, stored in RNAlater, and RNA was isolated using the QIASymphony kit. Poly-A pull-down was used for mRNA enrichment. Libraries were prepared using Illumina TruSeq RNA Prep Kit, and sequenced on Illumina HiSeq2500/HiSeq4000.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Description

AR125
CT40-s125

Data processing

Bases were called with RTA (Illumina), and bcl2fastq.gz2 (version 2.17) was used for converting BCL to fastq.gz format, with adaptor trimming.
Reads were mapped to UCSC/mm10 using STAR (2.5.2b), and summarized to gene-level counts with featureCounts (v1.5.0-p3). One sample at embryonic day 18 and 12hr (E18.5) was removed from the dataset due to poor quality.
Genes that were not represented by more than five counts in at least two replicates were filtered out of downstream analysis. To correct for differences in sequencing depth, the data then underwent upper-quartile normalization by the betweenLaneNormalization function from the EDASeq package. Removal of unwanted variation (RUV) normalization was performed by the RUVg function from the RUVSeq package, which uses factor analysis and a list of in silico empirical negative control genes to reduce variation from unknown technical effects.
Empirical controls, which can be considered non-rhythmic transcripts, were obtained by first-pass meta2d analysis using MetaCycle on the upper-quartile-normalized dataset (settings: cycMethod = c("JTK", "LS"), minper = 20, maxper = 28).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including count values for each sample and rhythmic analysis of transcripts using MetaCycle (v.1.2.0). Results ranked by decreasing integrated q-value (FDR-adusted p-value).

Submission date

Apr 10, 2020

Last update date

Apr 15, 2020

Contact name

Rosemary V Sampogna

E-mail(s)

[email protected]

Organization name

Columbia University

Department

Medicine