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Sample GSM7655000 Query DataSets for GSM7655000
Status Public on Sep 25, 2023
Title Donor_H_Vd1_PD1_pos
Sample type RNA
 
Source name Human breast skin
Organism Homo sapiens
Characteristics individual: Donor_H
age: 19
gender: Female
cell type: Vd1_PD1_pos
cell sort and lysis: Following culture, cell population indicated in column A was FACS sorted and lysed in RLT at a concentration of ~1667 cells/ul
Growth protocol Cultured human skin cells expanded for a total of 6 weeks in human IL-2 and IL15: 3mm punch biopsies obtained from discarded abdominal skin following elective plastic/reconstructive surgery were placed on tantalum coated grids and cultured in medium supplemented with human IL-2 and IL-15 for 3 weeks(Grid isolation). The cells were then taken 'off the grids' and cultured for a further 3 weeks in medium supplemented with human IL-2 and IL-15 (expansion phase).
Extracted molecule total RNA
Extraction protocol Cells were stained with a live dead exclusion dye and human antibodies specific for PD-1, CD3, TCRab, Vd1, CD8a and Pan gd. PD-1+ and PD-1- CD8 ab T cell and Vd1+ gd T cells were FACS sorted and lysed in RLT lysis buffer
Label None
Label protocol n/a
 
Hybridization protocol 8 ul of lysed cells (except sample Donor_A_Vd1_PD1_pos where 4ul was run) were hybridised at 65 degrees celcius overnight to NanoString's human nCounter Immune exhaustion panel
Scan protocol Hybridized samples were processed on an nCounter prep station (NanoString Technologies) following manufacturer's instructions.
Description ~13336 lysed cells in 8ul RLT buffer was hybridised to the nCounter panel at 65 degrees overnight.
Data processing Data were collected on an nCounter digital analyzer (NanoString Technologies), following manufacturer’s instructions. Using nSolver 4.0 (NanoString Technologies), raw counts were scaled based on the geometric mean of all positive control probes. Gene expression normalization (normalised counts) was performed relative to the geometric mean of all housekeeping genes included in the panel. The lower limit of detection was set at a normalised count of 20 which encompassed all negative control reference probes.
 
Submission date Jul 20, 2023
Last update date Sep 25, 2023
Contact name Shraddha Kamdar
E-mail(s) shraddha.kamdar@kcl.ac.uk
Organization name King’s College London
Department Peter Gorer Department of Immunobiology
Lab Immunosurveillance Lab
Street address Guys Hospital,Great Maze Pond, London Bridge
City London
ZIP/Postal code SE1 9RT
Country United Kingdom
 
Platform ID GPL33412
Series (1)
GSE232529 PD-1 defines a distinct, functional, tissue-adapted state in Vδ1+ T cells with implications for cancer immunotherapy

Data table header descriptions
ID_REF
VALUE Scaled and Normalized signal intensity computed using nSolver4.0 (NanoString Technologies).

Data table
ID_REF VALUE
ACACA null
ACADL null
ACADVL 2848.93
ACAT2 210.54
ACOT1/2 null
ACSL3 63.96
ACSL4 111.93
ACSL6 null
ADH1A/B/C null
ADH6 null
ADORA2A 714.23
ADORA2B null
AHR 562.32
AIFM1 117.26
AK4 231.86
AKT1 551.66
AKT2 751.54
AKT3 207.87
ALDH1A1 null
ALDH1A3 null

Total number of rows: 785

Table truncated, full table size 9 Kbytes.




Supplementary file Size Download File type/resource
GSM7655000_20230704_210426061024_DonorH-Vd1-PD1-pos_08.RCC.gz 8.8 Kb (ftp)(http) RCC
Processed data included within Sample table
Processed data are available on Series record

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