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Sample GSM1622795

Query DataSets for GSM1622795

Status

Public on Dec 31, 2021

Title

A1_1_S24

Sample type

SRA

Source name

neural stem cells

Organism

Mus musculus

Characteristics

tissue: subventricular zone
age: 7-month
sample type: Single cell
cell type: neural stem cells (NSCs)
Stage: qNSC

Extracted molecule

total RNA

Extraction protocol

Briefly, single cells were lysed in 5 μl lysis buffer and 1 μl of 3’ SMART CDS primer (24 μM) was added and incubated at 72°C for 3 min.
SMARTer Ultra Low Input RNA- High Volume kit was used to prepare amplified cDNA. We added 50 μl of nuclease-free H2O to the amplified cDNA to make a total volume of 60 μl. The cDNA was sheared in a microtube (6x 16mm) with 10% duty cycle, 5% intensity and 200 burst cycle for 5 min in the frequency sweeping mode with Covaris S2 machine. We got the average of 180 bp cDNA fragments after sonication. The illumina sequencing libraries were prepared using NEBNext Ultra DNA library prep kit.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Raw reads data are mapped to mm9 transcriptome with Bowtie1.0.0. Default paramters are used
TPM were generated by RSEM (1.2.15) with default parameters
Cells were filtered basing on the number of genes detected, cells have more than 4500 genes are discarded for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: geneTPM.txt includes TPM values for each Sample

Submission date

Mar 03, 2015

Last update date

Dec 31, 2021

Contact name

Haikun Liu

E-mail(s)

l.haikun@dkfz.de

Organization name

DKFZ

Street address

INF 581