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Sample GSM821264 Query DataSets for GSM821264
Status Public on Jan 11, 2012
Title second_trimester_euploid_AF_normalAFstudy_female3
Sample type RNA
 
Source name second_trimester_euploid_AF_normalAFstudy_female
Organism Homo sapiens
Characteristics gender: female
developmental stage: fetus
rna source: cell free mRNA from second trimester amniotic fluid
Extracted molecule total RNA
Extraction protocol RNA was extracted from 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).
Label biotin
Label protocol Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN, San Carlos, CA).
 
Hybridization protocol Arrays were washed and stained with streptavidin-phycoerythrin.
Scan protocol Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
Description femaleAF3
gene expression data from normal second trimester fetus
Data processing Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
 
Submission date Oct 24, 2011
Last update date Jan 11, 2012
Contact name Donna K Slonim
E-mail(s) Donna.Slonim@tufts.edu
Organization name Tufts University
Department Computer Science
Street address 161 College Ave.
City Medford
State/province MA
ZIP/Postal code 01845
Country USA
 
Platform ID GPL570
Series (1)
GSE33168 The amniotic fluid transcriptome: a source of novel information about human fetal development
Relations
Reanalysis of GSM406286

Data table header descriptions
ID_REF
VALUE Log-scale expression values produced by the Tukey-biweight summary method from the AffyPLM package.
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
1007_s_at 0.211146607 A 0.992457088
1053_at 1.952816008 A 0.52061967
117_at 4.128806681 P 0.017000453
121_at 3.293730846 A 0.066864977
1255_g_at 0.179005315 A 0.910594922
1294_at 1.508486023 A 0.378184515
1316_at 4.735259068 P 0.00868917
1320_at 1.550362054 A 0.52061967
1405_i_at 0.576686611 A 0.512520072
1431_at 1.736928346 A 0.438360878
1438_at 1.484773501 A 0.781016771
1487_at 2.880892836 A 0.127645309
1494_f_at 2.083898567 A 0.26746256
1552256_a_at 0.206697074 A 0.856998271
1552257_a_at 2.834419628 A 0.164032396
1552258_at 2.11455163 A 0.077429964
1552261_at 0.174538877 A 0.761546785
1552263_at -0.583470107 A 0.638946097
1552264_a_at 1.166870112 A 0.429431532
1552266_at 1.022958829 A 0.500000024

Total number of rows: 54675

Table truncated, full table size 1963 Kbytes.




Supplementary file Size Download File type/resource
GSM821264_femaleAF3.cel.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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