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| Status |
Public on Aug 01, 2019 |
| Title |
Taf1_14_prb |
| Sample type |
SRA |
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| Source name |
TAF1_Affected_Proband_Whole blood
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| Organism |
Homo sapiens |
| Characteristics |
subject group: TAF1 syndrome cohort
disease status: Affected
family status: Proband
tissue: Whole blood
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| Treatment protocol |
Globin mRNA was depleted from the samples using the GLOBINclear Kit (Life Technologies).
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
296898_S1
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| 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
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| Submission date |
Jul 27, 2016 |
| Last update date |
Aug 01, 2019 |
| Contact name |
Sara Ballouz |
| Organization name |
UNSW
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| Street address |
High St
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| City |
Kensington |
| State/province |
NSW |
| ZIP/Postal code |
2052 |
| Country |
Australia |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE84891 |
Expression analysis of the TAF1 syndrome |
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| Relations |
| BioSample |
SAMN05448779 |
| SRA |
SRX1979683 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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