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| Status |
Public on Sep 11, 2021 |
| Title |
lib55097 |
| Sample type |
SRA |
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| Source name |
Whole Blood
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| Organism |
Homo sapiens |
| Characteristics |
registry: Control
age at draw: 8
Sex: female
tissue: Whole Blood
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| Growth protocol |
Whole blood was collected in Tempus tubes (Ambion).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from whole blood samples using MagMax for Stabilized Blood Tubes RNA Isolation Kit (Ambion) and globin-reduced using GLOBINclear (Ambion) per manufacturer's instructions.
Globin-reduced RNA was used to construct libraries using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), with reverse transcription followed by PCR amplification to generate full length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.
Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies). Sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer (Illumina) with paired-end 53-base reads, using NextSeq P2 sequencing kits (Illumina) with a target depth of 5 million reads per sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Description |
lib55097_AAAHMLVM5
53_rn401506490
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| Data processing |
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned using the STAR aligner with the GRCh38 reference genome
Gene counts were generated using HTSeq-count (v0.4.1)29. Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Genome_build: GRCh38 reference genome and gene annotations from ensembl release 77
Supplementary_files_format_and_content: Processed data is in .csv format. Each row is a gene, each column is a sample.
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| Submission date |
Sep 08, 2021 |
| Last update date |
Apr 25, 2024 |
| Contact name |
Stephanie Osmond |
| E-mail(s) |
sosmond@benaroyaresearch.org
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| Organization name |
Benaroya Research Institute
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| Street address |
1201 9th Ave
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| City |
Seattle, |
| State/province |
WA |
| ZIP/Postal code |
98101 |
| Country |
USA |
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| Platform ID |
GPL30173 |
| Series (1) |
| GSE183701 |
Permutational immune analysis reveals architectural similarities between inflammaging, Down syndrome and autoimmunity |
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| Relations |
| BioSample |
SAMN21359630 |
| SRA |
SRX12109237 |
| 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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