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| Status |
Public on Dec 31, 2015 |
| Title |
4_CD4- ILC1 |
| Sample type |
SRA |
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| Source name |
sorted CD4- ILC1
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| Organism |
Homo sapiens |
| Characteristics |
cohort: Control; healthy control subject
age (yrs): 48
gender: Female
tissue: Peripheral blood
cell type: sorted CD4- ILC1
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cell subsets were sorted, then lysed to release RNA, converted to cDNA, and amplified using the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech)
Sequencing libraries were constructed from the amplified cDNA using a modified protocol of the Nextera XT DNA sample preparation kit (Illumina), to generate Illumina-compatible libraries.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Samples 3-4 are from the same subject
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| Data processing |
Base-calling was performed automatically in Illumina BaseSpace after sequencing; FASTQ reads were trimmed in Galaxy using FastqMcf (FastqMcf tool, v.1.0.0) to remove SMARTer adapter sequences
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0).
Reads representing potential PCR duplicates were removed in Galaxy using SAMTools rmdup (rmdup tool, v.1.0.1)
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Samples with low total raw counts (< 50,000; samples '13_CD4+ ILC1' and '14_CD4- ILC1') were removed prior to analysis.
Standard workflow in DESeq2 was followed to compare CD4+ vs. CD4- in ILC1 libraries using raw counts. Default values for normalization, calculating dispersion, and fitting the model were used in the DESeq function. Similarly, default values for filtering, based on low counts and outliers using Cook's distance, were used in the results function.
Genome_build: GRCh37
Supplementary_files_format_and_content: ILC1rawCounts.csv: comma-separated matrix – first column contains Ensembl gene ID, remaining columns include raw read counts assigned for each library. Data represents all processing steps up to read counting, not including sample QC and analysis with DESeq2.
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| Submission date |
Jun 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Scott Presnell |
| E-mail(s) |
SPresnell@benaroyaresearch.org
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| Organization name |
Benaroya Research Institute
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| Street address |
1201 Ninth Avenue
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98101 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE69596 |
Gene expression analysis of CD4+ and CD4- ILC1 subsets by RNAseq |
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| Relations |
| BioSample |
SAMN03762184 |
| SRA |
SRX1050076 |
| 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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