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Sample GSM2835550

Query DataSets for GSM2835550

Status

Public on Oct 27, 2020

Title

p14 Mertk WT-4

Sample type

SRA

Source name

retinal pigmented epithelial cells

Organism

Mus musculus

Characteristics

strain: mixed c57Bl/6J and B6;129-Mertktm1Grl/J
age: P14
tissue: retinal pigment epithelium
Sex: female
genotype/variation: Mertk WT

Extracted molecule

total RNA

Extraction protocol

RNA was extracted with RNeasy qiagen kit per kit protocol starting at 2 hour post-light onset.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Library Prep. Briefly, total RNA is used to purify the poly-A containing mRNA molecules using oligo-dT attached magnetic beads. RNA is fragmented into small pieces. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Then, second strand cDNA is synthesized using DNA Polymerase I and RNase H. cDNA fragments then have a single "A" base added along with ligation of adapters. The products are then purified using magnetic beads and then PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

p14 Mertk WT-4
21-3

Data processing

align to genome with STAR
count reads mapping to genes with featureCounts
Genome_build: grcm38
Supplementary_files_format_and_content: gene counts, txt

Submission date

Oct 27, 2017

Last update date

Oct 27, 2020

Contact name

Stephen Turner

Organization name

Signature Science, LLC

Street address

1670 Discovery Drive

City

Charlottesville