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Sample GSM828678 Query DataSets for GSM828678
Status Public on Feb 15, 2012
Title rat siSupt4h
Sample type SRA
Source name striatal neural cells
Organism Rattus norvegicus
Characteristics cell type: striatal neural cells
genotype: ST14A
transfection: siSupt4h
Treatment protocol mammalian cells were transfected with NC siRNA or siSupt4h
Extracted molecule total RNA
Extraction protocol mRNA was purified by Dynabeads® mRNA Purification Kit from total RNA. Then they were fragmented and reverse-transcribed as double strand cDNA by Super-script double-stranded cDNA synthesis kit from Invitrogen (Cat. 11917-010). The DNA then was end-repaired. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 150bp-350 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. Libraries were sequencedfollowing the manufacturer's protocols.
Library strategy RNA-Seq
Library source non-genomic
Library selection other
Instrument model Illumina HiSeq 2000
Description RNA-seq
insert size is 150bp-350 bp
Data processing Raw data were uploaded to and RNA-Seq/Transcriptome-base quantification analyses were performed to the samples.
Submission date Nov 04, 2011
Last update date May 15, 2019
Contact name Ning Deng
Organization name Stanford University
Department Genetics Department
Lab Cohen Lab
Street address 300 Pasteur Drive, RmL-314
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platform ID GPL14844
Series (1)
GSE33497 The effects on transcriptome from absence of Spt4/Supt4h by RNA-seq
SRA SRX105290
BioSample SAMN00752516

Supplementary file Size Download File type/resource
GSM828678_Rat_B.sam.txt.gz 8.7 Gb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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