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Sample GSM1129242 Query DataSets for GSM1129242
Status Public on May 15, 2013
Title FFPE_Total
Sample type SRA
Source name human normal kidney section (Cybrdi)
Organism Homo sapiens
Characteristics total rna input: 1000 ng
rna state: formalin-fixed, paraffin-embedded (FFPE)
Extracted molecule total RNA
Extraction protocol Library construction method: Standard
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing **********************************************************************

Removed rRNA reads by aligning reads to rRNA transcripts using BWA version 0.6.1 using default parameters
We created a set of reads that did not map to rRNA to be used for further processing. To do this, reads where neither mate aligned to rRNA were extracted for further use using samtools 0.1.9 using the following commands: samtools view -S -b -f 4 -F 264 rRNA.sam > rRNA.1.bam; samtools view -S -b -f 8 -F 260 rRNA.sam > rRNA.2.bam; samtools view -S -b -f 12 -F 256 rRNA.sam > rRNA.3.bam
Output bam files were merged and reads were extracted using Picard
These reads were aligned to the UCSC transcriptome twice. The first alignment was done to create a set of uniquely mapped reads so that they could be downsampled to a fixed number of reads which are known to map to the transcriptome. This was done using bowtie version 0.12.7 allowing for one hit per read. The following parameters were used: -q --phred33-quals -v 2 -e 99999999 -l 25 -I 1 -X 1000 -p 16 -k 1 -m 200
This alignment was then downsampled to a fixed number of reads using Picard
The downsampled portion of the reads were then aligned to the UCSC transcriptome using bowtie version 0.12.7 allowing for multiple hits per read. This was the second, final alignment. The following parameters were used: bowtie -q --phred33-quals -v 2 -e 99999999 -l 25 -I 1 -X 1000 -p 15 -a -m 200
Transcripts and genes were quanitifed using RSEM version 1.1.17 run with default settings using the final Bowtie alignment
Genome_build: UCSC Genome Browser17 knownGene transcript dataset (version 05-Feb-2012)
Supplementary_files_format_and_content: Processed data files are tab-delimited files that consist of the transcripts per million (TPM) expression level values as calculated by RSEM. Results are calculated at the gene (sample_gene.txt) and isoform (sample_isoform.txt) file. Each file contains TPM values calculated for each of the three protocols for the sample (RNaseH, RiboZero, and Total RNA)
Submission date Apr 24, 2013
Last update date May 15, 2019
Contact name Joshua Z Levin
Organization name Broad Institute of MIT & Harvard
Street address 320 Charles Street
City Cambridge
State/province MA
ZIP/Postal code 02141
Country USA
Platform ID GPL16791
Series (1)
GSE40705 Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples
BioSample SAMN02056216
SRA SRX271885

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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