GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM1541268

Query DataSets for GSM1541268

Status

Public on Jan 29, 2015

Title

IPMN High Risk sample11

Sample type

RNA

Source name

Microdissected IPMN tissue

Organism

Homo sapiens

Characteristics

tissue: pancreas ductal epithelium
risk: High-risk IPMN tissue

Extracted molecule

total RNA

Extraction protocol

miRNeasy™ FFPE Isolation Kit (Qiagen)

Label

FAM

Label protocol

n/a

Hybridization protocol

according to manufacturer's procedures

Scan protocol

n/a

Description

microRNA data from High-risk IPMN tissue

Data processing

Data was processed using the software ABI Sequence Detection software v2.3 from Applied Biosystems. The cut off value for Ct was set in 32 cycles taking into account that these samples were pre-amplified. Therefore, for miRNAs with undetermined expression and Ct values higher than 32 cycles, the miRNA was considered as non-expressed. Ct for cycle threshold meaning the cycle in which the specific miRNA starts to be detected. ddCt for delta delta Ct, defined by the formula (Ct of the specific miRNA in the target sample-Ct of the endogenous control RNU44 in the target sample)-(Ct of the specific miRNA in the control sample-Ct of the endogenous control RNU44 in the control sample) for each human pancreas preparation. RQ for relative quantification, defined by the formula 2^-ddCt . Small nuclear RNA (RNU44) was used as endogenous control.

Submission date

Nov 07, 2014

Last update date

Jan 29, 2015

Contact name

Jennifer Permuth Wey

Organization name

Moffitt Cancer Center

Street address

12902 Magnolia Dr

City

Tampa

State/province

ZIP/Postal code

33612

Country

USA

Platform ID

GPL19394

Series (2)

GSE63102	MiRNA Expression Analysis of Intraductal Papillary Mucinous Neoplasms (IPMNs) of the Pancreas
GSE63105	Intraductal papillary mucinous neoplasms (IPMNs) of the pancreas

Data table header descriptions
ID_REF
VALUE	delta delta Ct=(Ct of the specific miRNA in the target sample-Ct of the endogenous control RNU44 in the target sample)-(Ct of the specific miRNA in the control sample-Ct of the endogenous control RNU44 in the control sample)

Data table
ID_REF	VALUE
hsa-let-7a-000377 (FAM,NFQ)	14.13882
hsa-let-7c-000379 (FAM,NFQ)	10.96644
hsa-let-7d-002283 (FAM,NFQ)	14.720478
hsa-let-7e-002406 (FAM,NFQ)	16.507791
hsa-let-7f-000382 (FAM,NFQ)	9.685537
hsa-let-7g-002282 (FAM,NFQ)	12.789
hsa-miR-1-002222 (FAM,NFQ)
hsa-miR-9-000583 (FAM,NFQ)	11.714723
hsa-miR-10a-000387 (FAM,NFQ)	12.833433
hsa-miR-10b-002218 (FAM,NFQ)	11.314943
hsa-miR-15a-000389 (FAM,NFQ)	15.330501
hsa-miR-15b-000390 (FAM,NFQ)	10.91126
hsa-miR-16-000391 (FAM,NFQ)	12.527015
hsa-miR-17-002308 (FAM,NFQ)	15.209476
hsa-miR-18a-002422 (FAM,NFQ)	15.810058
hsa-miR-18b-002217 (FAM,NFQ)	9.87242
hsa-miR-19a-000395 (FAM,NFQ)	6.24586
hsa-miR-19b-000396 (FAM,NFQ)
hsa-miR-20a-000580 (FAM,NFQ)	10.559404
hsa-miR-20b-001014 (FAM,NFQ)	3.871557

Total number of rows: 378

Table truncated, full table size 13 Kbytes.

Supplementary data files not provided

Processed data included within Sample table

Processed data are available on Series record