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Sample GSM3615136 Query DataSets for GSM3615136
Status Public on Sep 15, 2019
Title 3D HTR8 B
Sample type RNA
 
Source name Immortalized human extravillous trophoblast cells
Organism Homo sapiens
Characteristics culture condition: 3D spheroids
tissue: Placenta
Treatment protocol 96-well ultra-low attachment (ULA) plates (Corning) were used to promote the self-assembly of HTR8/SVneo cells into three-dimensional (3D) cellular spheroids. 2D monolayer samples were simply cultured on flat-bottom plates.
Growth protocol HTR8/SVneo cells were cultured at 37°C in a humidified atmosphere of 5% CO2/95% atmospheric air in RPMI-1640 (Corning), supplemented with 5% heat-inactivated FBS (Gibco), 1% (v/v) penicillin-streptomycin (Corning) and 1% (v/v) L-glutamine (Corning). Media was replaced every two days, and at 70-80% confluency, HTR8/SVneo cells were sub-divided.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cells using TRIzol Reagent (Invitrogen) and Direct-zol RNA MiniPrep Kit (Zymo Research), following the manufacturer’s protocol.
Label Biotin
Label protocol 200 ng of RNA was processed and labelled with Biotin Allonamide Triphosphate.
 
Hybridization protocol Samples were hybridized for 16 hr at 45°C using Affymetrix WT PLUS Kit.
Scan protocol Affymetrix GeneChip™ 3000 instrument system
Data processing Normalization and output file generation was performed with Affymetrix Gene Expression Console (Thermo) using the Robust Multi-Chip Analysis (RMA) algorithm [RMA-Gene-full].
 
Submission date Feb 21, 2019
Last update date Sep 15, 2019
Contact name Michael Wong
E-mail(s) wongm20@mcmaster.ca
Organization name McMaster University
Street address 1200 Main Street West, Health Sciences Building
City Hamilton
State/province Ontario
ZIP/Postal code L8N 3Z5
Country Canada
 
Platform ID GPL23159
Series (1)
GSE126844 Transcriptomic analysis of human extravillous trophoblast cells (HTR8/Svneo) cultured as 3D spheroids and 2D monolayers

Data table header descriptions
ID_REF
VALUE Quantification

Data table
ID_REF VALUE
AFFX-BkGr-GC03_st 6.47744
AFFX-BkGr-GC04_st 6.81909
AFFX-BkGr-GC05_st 6.60996
AFFX-BkGr-GC06_st 6.41476
AFFX-BkGr-GC07_st 6.15672
AFFX-BkGr-GC08_st 4.07087
AFFX-BkGr-GC09_st 3.45513
AFFX-BkGr-GC10_st 3.09478
AFFX-BkGr-GC11_st 2.8145
AFFX-BkGr-GC12_st 2.6456
AFFX-BkGr-GC13_st 2.4625
AFFX-BkGr-GC14_st 2.41683
AFFX-BkGr-GC15_st 2.39066
AFFX-BkGr-GC16_st 2.54236
AFFX-BkGr-GC17_st 2.59753
AFFX-BkGr-GC18_st 2.82049
AFFX-BkGr-GC19_st 5.74946
AFFX-BkGr-GC20_st 5.79628
AFFX-BkGr-GC21_st 6.01703
AFFX-BkGr-GC22_st 6.01723

Total number of rows: 24351

Table truncated, full table size 635 Kbytes.




Supplementary file Size Download File type/resource
GSM3615136_HCS_101818H_SR6_3D_HTR8_B.CEL.gz 1016.2 Kb (ftp)(http) CEL
GSM3615136_HCS_101818H_SR6_3D_HTR8_B.sst-rma-gene-full.chp.gz 173.0 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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