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Sample GSM1901313

Query DataSets for GSM1901313

Status

Public on Dec 11, 2015

Title

22yo ctx astro

Sample type

SRA

Source name

Adult temporal lobe

Organism

Homo sapiens

Characteristics

age: 22 years old
cell subtype: HepaCAM positive cells
cell type: Astrocyte

Extracted molecule

total RNA

Extraction protocol

Tissue was dissociated in papain (30units / ml) for 1.5 hours before trituration. Cells were immunopanned on a sequence of plates in the following order: CD45 --> GalC --> GalC --> Thy1 --> HepaCAM. Cells bound to HepaCAM plate were then scraped in Qiazol to harvest RNA
Nugen Ovation V2 kit (7102-32), followed by sonication in the Covaris machine, followed by indexing with NEB Next Ultra kit (E7530L)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Data processing

The FASTQ files were first groomed using the FASTQ groomer and then mapped using TopHat2, which invokes Bowtie as an internal read mapper (Trapnell et al., 2009). The paired end option was selected and human genome version 19 (hg19) was used as the reference genome. We then ran Cufflinks to assemble transcripts and estimate expression level as fragments per kilobase of transcript sequence per million mapped fragments (FPKM) (Trapnell et al., 2010).
Genome_build: Hg19 or mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

Submission date

Oct 04, 2015

Last update date

May 15, 2019

Contact name

Steven Sloan

E-mail(s)

sasloan@emory.ed

Phone

9412280511

Organization name

Emory University