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| Status |
Public on Jul 09, 2018 |
| Title |
4N_NEXTflex.Lab8.SynthEQ |
| Sample type |
SRA |
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| Source name |
Synthetic smallRNA; Equimolar Pool
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| Organism |
synthetic construct |
| Characteristics |
lab: Lab8
lib.method.detail: 4N_NEXTflex
lib.method.simple: 4N
pool: SynthEQ
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| 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.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| 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 "|".
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| Submission date |
Feb 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Muneesh Tewari |
| E-mail(s) |
mtewari@med.umich.edu
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| Organization name |
University of Michigan
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| Lab |
4029 BSRB
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| Street address |
109 Zina Pitcher Pl
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109-2200 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN06309316 |
| SRA |
SRX2541789 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2478873_sample_Eq_Alt_1_AGTCAA_L001_R1_001_fastq.clipped.trimmed.filtered.calibratormapped.counts.txt.gz |
6.0 Kb |
(ftp)(http) |
TXT |
| GSM2478873_sample_Eq_Alt_1_AGTCAA_L001_R1_001_fastq_readCounts_miRNAmature_sense.txt.gz |
8.0 Kb |
(ftp)(http) |
TXT |
| GSM2478873_sample_Eq_Alt_2_AGTTCC_L001_R1_001_fastq.clipped.trimmed.filtered.calibratormapped.counts.txt.gz |
6.4 Kb |
(ftp)(http) |
TXT |
| GSM2478873_sample_Eq_Alt_2_AGTTCC_L001_R1_001_fastq_readCounts_miRNAmature_sense.txt.gz |
8.9 Kb |
(ftp)(http) |
TXT |
| GSM2478873_sample_Eq_Alt_3_ATGTCA_L001_R1_001_fastq.clipped.trimmed.filtered.calibratormapped.counts.txt.gz |
6.5 Kb |
(ftp)(http) |
TXT |
| GSM2478873_sample_Eq_Alt_3_ATGTCA_L001_R1_001_fastq_readCounts_miRNAmature_sense.txt.gz |
8.9 Kb |
(ftp)(http) |
TXT |
| GSM2478873_sample_Eq_Alt_4_CCGTCC_L001_R1_001_fastq.clipped.trimmed.filtered.calibratormapped.counts.txt.gz |
6.5 Kb |
(ftp)(http) |
TXT |
| GSM2478873_sample_Eq_Alt_4_CCGTCC_L001_R1_001_fastq_readCounts_miRNAmature_sense.txt.gz |
9.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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