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Sample GSM7802557 Query DataSets for GSM7802557
Status Public on Apr 24, 2024
Title T.9.C1
Sample type RNA
 
Source name CD3+ selected leukapheresis, patient
Organism Homo sapiens
Characteristics disease state: large B-cell lymphoma
model (1: EXP, 2: poor-EXP): 1
cell type: CD3+ selected leukapheresis, patient
Treatment protocol Leukapheresis samples and donor lymphocyte infusions were quickly thawed and CD3+ cells were selected using magnetic anti-CD3 microbeads (Miltenyi Biotec) and the autoMACS Pro Separator (Miltenyi Biotec)
Growth protocol n/a
Extracted molecule total RNA
Extraction protocol RNA was extracted from CD3-positive selected cells with miRNeasy Mini kit (Qiagen) and 100 ng of total RNA were used for the transcriptomic analyses
Label n/a
Label protocol Probe labeling was performed according to Nanostring manufacturer's protocol
 
Hybridization protocol Hybridization was performed according to Nanostring manufacturer's protocol, overnight at 65°C, 18h in a thermocycler
Scan protocol Cartridges were run on a nCounter Nanostring machine
Data processing NanoStringNorm package for R software 4.1.2 (R Foundation for Statistical Computing, Vienna, Austria) was used to generate data and for quality check; the geometric mean of the counts relative to each sample, the mean plus two standard deviations and the total sum of counts options were used to correct the data for technical, background, and batch-effect issues, respectively.
 
Submission date Sep 25, 2023
Last update date Apr 24, 2024
Contact name Luca Agnelli
E-mail(s) luca.agnelli@istitutotumori.mi.it, luca.agnelli@gmail.com
Phone +390223903581
Organization name IRCCS Istituto Nazionale dei Tumori
Department Department of Advanced Diagnostics
Street address Venezian 1
City MILAN
ZIP/Postal code 20133
Country Italy
 
Platform ID GPL29417
Series (1)
GSE243973 Circulating monocyte counts coupled with a 4-gene signature at leukapheresis predict survival of lymphoma patients treated with CAR T

Data table header descriptions
ID_REF
VALUE normalized signal intensity

Data table
ID_REF VALUE
NCR3 7.703
CCL5 12.24
ACOT2 7.405
PFKP 9.59
NOD2 7.621
AKT1 8.82
TRBV7-6 6.539
PDK3 8.877
IL5 0
CCL8 0
CD1A 0
PPAT 7.662
PPT2 6.499
IL3RA 0
IFI30 10.99
HACD4 9.278
TOMM6 9.327
MID1IP1 7.825
HK3 2.922
STAT5A 10.07

Total number of rows: 794

Table truncated, full table size 8 Kbytes.




Supplementary file Size Download File type/resource
GSM7802557_T.9.C1.RCC.gz 8.9 Kb (ftp)(http) RCC

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