Result

Search results for the GEO ID: GSE39227

(Click on the check boxes provided under "Select for analysis", to initiate grouping)

(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down)

GSM ID

GPL ID

Select for analysis

Title

Source name

Description

Characteristics

GSM958399

GPL570

cell line_293T_Ago2-IP_control

cell line 293T

cell line: 293T transfected with: scrambled oligo genotype/variation: control ip antibody: nonimmune IgG beads ip antibody vendor: millipore ip antibody cat. #: 17-700 ip antibody lot. #: NG1682636

Ago2-IP after mock transfection

Sample_geo_accession	GSM958399
Sample_status	Public on Dec 20 2012
Sample_submission_date	Jul 10 2012
Sample_last_update_date	Dec 20 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Ago2 Immunoprecipitation (Ago2-IP) experiments after miR-941 overexpression were conducted in 293T cell line. Briefly, All transfections were performed using human 293T cells cultured in 6-well tissue culture plates. Lipofectamine 2000 (Invitrogen) was used for a Synthetic miR-941 or a scrambled oligo transfection, at 30 nmol/l each (final concentration) per 1x106 cells/well of a 6-well plate using DharmaFECT (GE Healthcare). Total 5x106 cells were collected and subjected to Ago2 immunoprecipitation (Ago2-IP) using the RNA isolation kit Mouse Ago2 (Wako Chemicals) according to the manufacturer's instructions. For a negative control, immunoprecipitation was performed using nonimmune IgG beads prepared with the antibody immobilization bead kit (Wako Chemicals). The IP pull down RNA was used as template for an “in vitro” transcription reaction generating biotin-labeled antisense cRNA. The cRNA was analyzed on affymetrix Human Genome U133 Plus 2.0 arrays following the manufacturer’s instructions.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA were extracted with Trizol reagent (Invitrogen).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Labeling was performed according to standard Affymetrix protocols.
Sample_hyb_protocol	Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays.
Sample_scan_protocol	Affymetrix Gene ChIP Scanner 3000 7G
Sample_data_processing	RMA processing was used to generate expression levels for the probesets. It includes quantile normalization and log2 transformation (R Affy package). MAS5 was used as well to return 'Present/Absent/Marginal' flags and p-values on each probeset, which can be used for filtering ('pam' and 'pvalue' in the data table).
Sample_platform_id	GPL570
Sample_contact_name	Song,,Guo
Sample_contact_institute	PICB
Sample_contact_address	320 Yue Yang Road
Sample_contact_city	shanghai
Sample_contact_zip/postal_code	200031
Sample_contact_country	China
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM958nnn/GSM958399/suppl/GSM958399_cell_line_293T_Ago2-IP_control.CEL.gz
Sample_series_id	GSE35621
Sample_series_id	GSE39227
Sample_data_row_count	54675

GSM958400

GPL570

cell line_293T_Ago2-IP_miR941

cell line 293T

cell line: 293T transfected with: Synthetic miR-941 genotype/variation: miR-941 overexpression ip antibody: Ago2 ip antibody vendor: Wako Chemicals ip antibody cat. #: 292-66701 ip antibody lot. #: LAJ5512

Ago2-IP after miR941 transfection

Sample_geo_accession	GSM958400
Sample_status	Public on Dec 20 2012
Sample_submission_date	Jul 10 2012
Sample_last_update_date	Dec 20 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Ago2 Immunoprecipitation (Ago2-IP) experiments after miR-941 overexpression were conducted in 293T cell line. Briefly, All transfections were performed using human 293T cells cultured in 6-well tissue culture plates. Lipofectamine 2000 (Invitrogen) was used for a Synthetic miR-941 or a scrambled oligo transfection, at 30 nmol/l each (final concentration) per 1x106 cells/well of a 6-well plate using DharmaFECT (GE Healthcare). Total 5x106 cells were collected and subjected to Ago2 immunoprecipitation (Ago2-IP) using the RNA isolation kit Mouse Ago2 (Wako Chemicals) according to the manufacturer's instructions. For a negative control, immunoprecipitation was performed using nonimmune IgG beads prepared with the antibody immobilization bead kit (Wako Chemicals). The IP pull down RNA was used as template for an “in vitro” transcription reaction generating biotin-labeled antisense cRNA. The cRNA was analyzed on affymetrix Human Genome U133 Plus 2.0 arrays following the manufacturer’s instructions.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA were extracted with Trizol reagent (Invitrogen).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Labeling was performed according to standard Affymetrix protocols.
Sample_hyb_protocol	Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays.
Sample_scan_protocol	Affymetrix Gene ChIP Scanner 3000 7G
Sample_data_processing	RMA processing was used to generate expression levels for the probesets. It includes quantile normalization and log2 transformation (R Affy package). MAS5 was used as well to return 'Present/Absent/Marginal' flags and p-values on each probeset, which can be used for filtering ('pam' and 'pvalue' in the data table).
Sample_platform_id	GPL570
Sample_contact_name	Song,,Guo
Sample_contact_institute	PICB
Sample_contact_address	320 Yue Yang Road
Sample_contact_city	shanghai
Sample_contact_zip/postal_code	200031
Sample_contact_country	China
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM958nnn/GSM958400/suppl/GSM958400_cell_line_293T_Ago2-IP_miR941.CEL.gz
Sample_series_id	GSE35621
Sample_series_id	GSE39227
Sample_data_row_count	54675

Make groups for comparisons

(2 groups will be compared at a time)

Select GSMs and click on "Add groups"

Enter the group name here:

Select expression type

Transcripts profile based on;

A. Differential status (Up/Down regulation)

B. Absolute calls (Transcribed/Not-detected)

Filter results by number of probes