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Sample GSM2478886 Query DataSets for GSM2478886
Status Public on Jul 09, 2018
Title TruSeq.Lab9.SynthEQ
Sample type SRA
 
Source name Synthetic smallRNA; Equimolar Pool
Organism synthetic construct
Characteristics lab: Lab9
lib.method.detail: TruSeq
lib.method.simple: TruSeq
pool: SynthEQ
Extracted molecule other
Extraction protocol The RNA sample was provided as a single aliquot containing all the synthetic RNAs. 10 femtomoles of the RNA pool was used as input for each library.
Library construction protocols varied by sample (See lib.method.simple and lib.method.detail sample characteristics). TruSeq, CleanTag, NEBNext and 4N_NEXTflex protocols use the commercial kits and were optimized for sequencing of small RNAs from low-input biosamples. 4N_A, _B, _C and _D are in-house protocols using 5' and 3' adapters with 4N randomized terminal nucleotides.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
 
Data processing All FASTQ files were processed through the exceRpt small RNA-seq pipeline using the Genboree Workbench tools (http://genboree.org/java-bin/workbench.jsp). Default parameters were used, except for changing "minimum read length" to 15, and uploading the FASTQ file with the synthetic pool sequences as a "Spike-in". For the subset of "4N" libraries, the "Random Barcodes Present in Samples" option was checked, and the corresponding default subsettings were used (barcode length = 4; barcode location -5p and -3p).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_fastq_readCounts_miRNAmature_sense.txt: Mature miRNA Read Counts: Tab-delimited text files contain counts for genomic alignments to known human miRNAs, including only reads mapping in the same orientation as the indicated miRNA. For each miRNA, counts are provided to indicate i) number of unique reads, ii) total reads and iii) total reads, adjusted for ambiguous mapping to other genomic loci. Libraries generated using 4N adapters have an additional column that includes the number of unique random barcodes, also adjusted for multi-mapping. Our study used the "multimapAdjustedReadCount" column for all our calculations.
Supplementary_files_format_and_content: *_fastq.clipped.trimmed.filtered.calibratormapped.counts.txt: Mapped Calibrator Counts: Tab-delimited text files contain the name of the synthetic RNA in column 1, and mapped read counts in the second. The sequence ID contains the equimolar and ratiometric pool IDs, if present in both pools; an "NA", if not. The ratiometric pool ID contains the name of the sequence, relative concentration in pool A and relative concentration in pool B, delimited by "|".
 
Submission date Feb 06, 2017
Last update date May 15, 2019
Contact name Muneesh Tewari
E-mail(s) mtewari@med.umich.edu
Organization name University of Michigan
Lab 4029 BSRB
Street address 109 Zina Pitcher Pl
City Ann Arbor
State/province MI
ZIP/Postal code 48109-2200
Country USA
 
Platform ID GPL19604
Series (2)
GSE94584 Systematic assessment of next-generation sequencing for quantitative small RNA profiling: synthetic equimolar pool
GSE94586 Systematic assessment of next-generation sequencing for quantitative small RNA profiling: a multiple protocol study across multiple laboratories
Relations
BioSample SAMN06309303
SRA SRX2541802

Supplementary file Size Download File type/resource
GSM2478886_sample_Illumina_RPI25_ACTGATAGTTCAGA_L078_R1_001_fastq.clipped.trimmed.filtered.calibratormapped.counts.txt.gz 8.5 Kb (ftp)(http) TXT
GSM2478886_sample_Illumina_RPI25_ACTGATAGTTCAGA_L078_R1_001_fastq_readCounts_miRNAmature_sense.txt.gz 11.5 Kb (ftp)(http) TXT
GSM2478886_sample_Illumina_RPI26_ATGAGCAGTTCAGA_L078_R1_001_fastq.clipped.trimmed.filtered.calibratormapped.counts.txt.gz 8.4 Kb (ftp)(http) TXT
GSM2478886_sample_Illumina_RPI26_ATGAGCAGTTCAGA_L078_R1_001_fastq_readCounts_miRNAmature_sense.txt.gz 11.3 Kb (ftp)(http) TXT
GSM2478886_sample_Illumina_RPI27_ATTCCTAGTTCAGA_L078_R1_001_fastq.clipped.trimmed.filtered.calibratormapped.counts.txt.gz 8.3 Kb (ftp)(http) TXT
GSM2478886_sample_Illumina_RPI27_ATTCCTAGTTCAGA_L078_R1_001_fastq_readCounts_miRNAmature_sense.txt.gz 10.7 Kb (ftp)(http) TXT
GSM2478886_sample_Illumina_RPI28_CAAAAGAGTTCAGA_L078_R1_001_fastq.clipped.trimmed.filtered.calibratormapped.counts.txt.gz 8.2 Kb (ftp)(http) TXT
GSM2478886_sample_Illumina_RPI28_CAAAAGAGTTCAGA_L078_R1_001_fastq_readCounts_miRNAmature_sense.txt.gz 10.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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