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Sample GSM2809222

Query DataSets for GSM2809222

Status

Public on Oct 13, 2017

Title

Jag1+/+ rep 2

Sample type

SRA

Source name

Jag1+/+_liver

Organism

Mus musculus

Characteristics

strain background: C3H/C57bl6J
genotype/variation: Jag1+/+
developmental stage: postnatal day 10
tissue: liver

Treatment protocol

No treatment.

Growth protocol

Livers collected at postnatal day 10.

Extracted molecule

polyA RNA

Extraction protocol

Mouse livers were collected fresh and stored in RNAlater® (cat. no. AM7020, Ambion) at -80 °C. RNA was extracted from one lobe using the RNeasy Mini Kit (cat. no. 74104, QIAGEN), including on-column DNase I digestion (cat. no. 79254, QIAGEN).
cDNA libraries for all samples were created using the TruSeq® RNA Sample Prep Kit v2–48, Set A (cat. no. RS-122-2001, Illumina®,) as per the TruSeq® RNA Sample Preparation v2 Guide, Low-Throughput Protocol.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

1329_1_Jag1wt
RPKM Jag1wt_rep2

Data processing

Reads were aligned using STAR to genome mm10
Reads with multiple alignments were removed
Gene expression values were calculated using rpkmforgenes.py (https://github.com/danielramskold/Allelic_patterns_in_clonal_somatic_cells) with options -rmnameoverlap -bothendsceil and using RefSeq annotation from February 2015
RPKM values were TMM normalized
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text of normalised expression values and read counts

Submission date

Oct 12, 2017

Last update date

May 15, 2019

Contact name

Urban Lendahl

Organization name

Karolinska Insttitutet

Street address

Von Eulers vag 3

City

Stockholm