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| Status |
Public on Feb 02, 2012 |
| Title |
kidney-AA-4 |
| Sample type |
SRA |
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| Source name |
aristolochic acid treated
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: kidney
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| Growth protocol |
six-week-old Big Blue rats were gavaged with 10 mg/kg body weight AA five times a week for 12 weeks and were sacrificed one day after of the last treatment. The animal tissues were isolated, frozen quickly in liquid nitrogen, and stored at -80°C.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Libraries were prepared according to Illumina's instructions for mRNA sequencing. Briefly, poly-A tailed mRNA was purified from total RNA with Sera-Mag Magnetic Oligo (dT) beads, and then was fragmented into small pieces using divalent cations under elevated temperature. Using reverse transcriptase and random primers, the cleaved RNA fragments were then used to synthesize the first and second strand cDNAs. The cDNA was treated in “end repair” reaction with T4 DNA polymerase and Klenow DNA polymerase to blunt ends. An “A” base was then added to the 3’ end of the blunt phosphorylated DNA fragments, and an Illumina adapter with a single “T” base overhang at its 3’ end was then ligated to the end of the DNA fragment, preparing it to be hybridized in a single read flow cell. After the ligation reaction, a size range of cDNA templates was selected and these fragments were amplified on a cluster station with single-read cluster generation kit v2. Finally, cDNA template clusters were sequenced on the Genome Analyzer II with SBS Sequencing Kit v3. Each RNA sample was sequenced in one lane, generating over 16 million reads of 36 bases long per sample. Images taken during the sequencing reactions were analyzed with Illumina software pipelines with base-calling done by Bustard, and sequence analysis performed with Gerald.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
RNA-Seq
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| Data processing |
30,941 unique rat RefSeq RNAs downloaded from NCBI blast database (ftp://ftp.ncbi.nlm.nih.gov/blast/db/refseq_rna.tar.gz) on November 30, 2009 as the reference annotation. The aligners used were bowtie-0.10.1 (http://sourceforge.net/projects/bowtie-bio/files/bowtie/), blastn/megablast (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.21/), and GeneSifter (http://www.geospiza.com/Products/AnalysisEdition.shtml). For bowtie, the default options were used to control the behavior of the aligner for sequence alignment except for options “-5 4 -3 10 -l 12”. The “-5 4” option trims four bases from the high-quality (left) end of each read before alignment, the “-3 10” controls the length of bases trimmed from the low-quality (right) end of reads, and the “-l 12” option controls the length of seeds which are the first 12 bases on the high-quality end of sequence reads. The maximum number of mismatches allowed in seeds is the default 2. For blastn, we used the default options except for the expectation value of 0.001; for megablast, we used an expectation value of 0.001 and word size of 12.
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| Submission date |
Apr 05, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhenqiang Su |
| E-mail(s) |
zhenqiangsu@gmail.com
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| Phone |
501-584-8331
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| Organization name |
Thomson Reuters
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| Department |
IP & Science
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| Street address |
22 Thomson Place
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02210 |
| Country |
USA |
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| Platform ID |
GPL10287 |
| Series (1) |
| GSE21210 |
Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic Acid on rat kidneys |
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| Relations |
| SRA |
SRX018815 |
| BioSample |
SAMN00010955 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM530342_AA_4_Blastn_gene.count.txt.gz |
148.1 Kb |
(ftp)(http) |
TXT |
| GSM530342_AA_4_GeneSifter_gene.count.txt.gz |
951.9 Kb |
(ftp)(http) |
TXT |
| GSM530342_AA_4_bowtie_gene.count.txt.gz |
98.2 Kb |
(ftp)(http) |
TXT |
| GSM530342_AA_4_megablast_gene.count.txt.gz |
80.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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