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| Status |
Public on Aug 22, 2020 |
| Title |
EoE-02.tRNA.EoE |
| Sample type |
SRA |
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| Source name |
esophageal tissue
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| Organism |
Homo sapiens |
| Characteristics |
study group: EoE
age: 75
eosinophils per high-powered field: 80
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| Growth protocol |
Biopsies were collected in RNAlater (Thermo Fisher Scientific) and paired blood samples were collected in Tempus Blood RNA Tubes (Thermo Fisher) and stored at -80◦C until use.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from adult esophageal biopsies (1-2 per subject) by homogenizing tissue in QIAzol lysis reagent (Qiagen) followed by column purification using the miRNeasy kit with on column DNA digestion (Qiagen). Whole blood RNA was extracted using MagMax for Stabilized Blood Tubes RNA Isolation Kit, followed by globin reduction using GlobinClear Human (Thermo Fisher).
Sequencing libraries were constructed from total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) and NexteraXT DNA sample preparation kit (Illumina) to generate Illumina- compatible barcoded libraries.
Dual-index, single-read sequencing of pooled libraries was carried out on a HiSeq2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS 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 |
Illumina HiSeq 2500 |
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| Description |
EREFS 3
lib29307_CCFMDANXX
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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 TopHat aligner (v1.4.1)28 with the GRCh38 reference genome and gene annotations from ensembl release 77.
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 (counts) are in .csv format. Each row is a gene, each column is a sample.
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| Submission date |
Aug 21, 2020 |
| 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 |
GPL16791 |
| Series (1) |
| GSE156651 |
Conserved interferon signature between adult and pediatric eosinophilic esophagitis |
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| Relations |
| BioSample |
SAMN15878153 |
| SRA |
SRX8984406 |
| 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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