 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 28, 2016 |
| Title |
T38-CXCR6p |
| Sample type |
SRA |
| |
|
| Source name |
Healthy liver leukocytes
|
| Organism |
Homo sapiens |
| Characteristics |
individual: patient T38
cell type: Eomes positive NK cells
|
| 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
|
| 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| 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
|
| |
|
| Submission date |
Sep 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Victoria Male |
| E-mail(s) |
v.male@imperial.ac.uk
|
| Organization name |
Imperial College London
|
| Street address |
Metabolism, Digestion and Reproduction, Imperial College London, Chelsea and Westminster Hospital Campus, 369 Fulham Road
|
| City |
London |
| State/province |
Not Applicable (Outside of US and Canada) |
| ZIP/Postal code |
SW10 9NH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE87392 |
Comparison of Eomes-negative and Eomes-positive human liver NK cells by RNASeq |
|
| Relations |
| BioSample |
SAMN05829380 |
| SRA |
SRX2193270 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2330099_T38Eomespostrimmedalignments.csv.gz |
91.5 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 |
|
|
|
|
 |
