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Sample GSM2253369 Query DataSets for GSM2253369
Status Public on Aug 01, 2019
Title Taf1_11_prb
Sample type SRA
 
Source name TAF1_Affected_Proband_Whole blood
Organism Homo sapiens
Characteristics subject group: TAF1 syndrome cohort
disease status: Affected
family status: Proband
tissue: Whole blood
Treatment protocol Globin mRNA was depleted from the samples using the GLOBINclear Kit (Life Technologies).
Extracted molecule total RNA
Extraction protocol RNA was precipitated with ammonium acetate, washed and resuspended in 14 µl TE (10 mM Tris-HCl pH 8, 1 mM EDTA).
For each sample 1.1 µg RNA were hybridized with the provided streptavidin beads and purified. 1 µl of a 1:100 dilution of ERCC RNA Spike-In control (Thermo Fisher) was added to 1 µg RNA and libraries generated according to the TruSeq Stranded mRNA Library Kit-v2 (Illumina).
Quality control of the generated libraries was performed on a Bioanalyzer High Sensitivity DNA chip (Agilent) and the concentration was measured using Qubit dsDNA HS Assay (Life Technologies). To eliminate primer dimers in the libraries, additional purifications were performed using the Agencourt AMPure XP system (Beckman Coulter). The libraries were pooled to 2-10 nM total concentration and sequenced on a NextSeq, PE100, mid output. Libraries were generated independently for each family and family-pools sequenced on separate lanes.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description 296732_S1
Data processing Base calling:
Artifacts filter: fastx_artifacts_filter -v -Q 33, (fastX toolbox)
Quality filter: fastq_quality_filter -v -Q 33 -q 30 -p 50 , (fastX toolbox),
Combine paired reads: fastQCombinePairedEnd.py (https://github.com/enormandeau/Scripts/blob/master/fastqCombinePairedEnd.py)
Alignment: STAR 2.4.2a, GENCODE v22 and GENCODEv24, parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outSAMtype None --quantMode GeneCounts --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0.66
Quantification: RSEM v1.2.29, GENCODE v22, parameters: rsem-calculate-expression --bam --no-bam-output --seed 12345 -p 8 --paired-end --forward-prob 0 [Aligned.toTranscriptome.out.bam] [RSEMGenome] Quant
Genome_build: GRCh38, GENCODE v22, v24
Supplementary_files_format_and_content: tab-delimited files, rows contain ensemblIDs for gene level counts, TPM, FPKM
 
Submission date Jul 27, 2016
Last update date Aug 01, 2019
Contact name Sara Ballouz
Organization name UNSW
Street address High St
City Kensington
State/province NSW
ZIP/Postal code 2052
Country Australia
 
Platform ID GPL18573
Series (1)
GSE84891 Expression analysis of the TAF1 syndrome
Relations
BioSample SAMN05448782
SRA SRX1979680

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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