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Status |
Public on Sep 28, 2016 |
Title |
T35-CXCR6p |
Sample type |
SRA |
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Source name |
Healthy liver leukocytes
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Organism |
Homo sapiens |
Characteristics |
individual: patient T35 cell type: Eomes positive NK cells
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Treatment protocol |
Leukocytes were isolated from the perfusion fluid of healthy human livers destined for transplant by density gradient centrifugation. Live Eomes- NK cells (propidium iodide negative, CD3-, CD56+, CXCR6-, CD16+) and Eomes+ NK cells (propidium iodide negative, CD3-, CD56+, CXCR6+) were sorted on a BD Aria
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from sorted cells using an RNeasy Micro Kit (Qiagen, Manchester, UK) and cDNA amplified using a SMART-Seq Ultra Low Input RNA kit for sequencing (Takara Bio Europe/Clontech, Saint-Germain-en-Laye, France). Amplified cDNA (200 pg) was used as input for library preparation using Nextera XT DNA Library Preparation Kit (Illumina, Essex, UK) with 12 cycles of PCR.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Data processing |
Basecalls were made using Illumina BaseSpace TrueSeq Amplicon 2.0 Alignments were performed against Homo sapiens/hg19 (RefSeq) using Illumina BaseSpace TopHat v2.1.0 Regularized log transformed normalization was performed using Illumina DESeq2 v1.0.0 Genome_build: hg19 Supplementary_files_format_and_content: csv files contain raw and normalized reads for each sample
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Submission date |
Sep 27, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Victoria Male |
E-mail(s) |
v.male@imperial.ac.uk
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Organization name |
Imperial College London
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Street address |
Metabolism, Digestion and Reproduction, Imperial College London, Chelsea and Westminster Hospital Campus, 369 Fulham Road
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City |
London |
State/province |
Not Applicable (Outside of US and Canada) |
ZIP/Postal code |
SW10 9NH |
Country |
United Kingdom |
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Platform ID |
GPL18573 |
Series (1) |
GSE87392 |
Comparison of Eomes-negative and Eomes-positive human liver NK cells by RNASeq |
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Relations |
BioSample |
SAMN05829384 |
SRA |
SRX2193266 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2330095_T35Eomespostrimmedalignments.csv.gz |
91.7 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
Processed data provided as supplementary file |
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