Result

Search results for the GEO ID: GSE43089

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM1056320

GPL1261

Wild type retina at E18

wild-type retina

strain/background: C57BL/6 genotype/variation: wild-type age: E18 tissue: retina

Embryo_Sox11_WT

Sample_geo_accession	GSM1056320
Sample_status	Public on Dec 28 2012
Sample_submission_date	Dec 20 2012
Sample_last_update_date	Dec 28 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Not applicable.
Sample_growth_protocol_ch1	Not applicable.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Retinaes were dissected from all littermate embryos, and all samples were genotyped. From each retina of WT and Sox11 mutant embryo, RNA was extracted by the RNeasy Plus Micro kit (QIAGEN), and cDNA synthesis and amplification were performed using the cDNA Synthesis and Amplification kit (Affymetrix).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	500ng of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol Rev.3 recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Affymetrix). Double-stranded cDNA was cleaned up by the Sample Cleanup Module (Affymetrix). In vitro transcription was performed on all cDNAs using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin columns (QIAGEN). The cRNA was fragmented by metal-induced hydrolysis.
Sample_hyb_protocol	10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controlled by adding cRNA cocktail (bioB, bioC, bioD, cre). Washing and staining were performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.
Sample_scan_protocol	Scanning was performed in an Affymetrix GeneChip® Scanner 3000 7G. Chip analysis was performed using the Affymetrix GeneChip® Operating Software v1.4.
Sample_data_processing	Affymetrix GeneChip Operating Software v1.4. The average values were scaled to 100 so that all chips could be directly compared.
Sample_platform_id	GPL1261
Sample_contact_name	Sumiko,,Watanabe
Sample_contact_email	sumiko@ims.u-tokyo.ac.jp
Sample_contact_phone	81 3 5449 5663
Sample_contact_fax	81 3 5449 5474
Sample_contact_laboratory	Department of Molecular and Developmentl Bioloty
Sample_contact_department	Institute of Medical Science
Sample_contact_institute	University of Tokyo
Sample_contact_address	4-6-1 Shirokane-dai
Sample_contact_city	Minato-ku, Tokyo
Sample_contact_zip/postal_code	108-8639
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1056nnn/GSM1056320/suppl/GSM1056320_Embryo_Sox11_WT_430.CEL.gz
Sample_series_id	GSE43089
Sample_data_row_count	45101

GSM1056321

GPL1261

Sox11 loss-of-function mutant retina at E18

Sox11 KO retina

strain/background: C57BL/6 genotype/variation: Sox11-/- age: E18 tissue: retina

Embryo_Sox11_KO

Sample_geo_accession	GSM1056321
Sample_status	Public on Dec 28 2012
Sample_submission_date	Dec 20 2012
Sample_last_update_date	Dec 28 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Not applicable.
Sample_growth_protocol_ch1	Not applicable.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Retinaes were dissected from all littermate embryos, and all samples were genotyped. From each retina of WT and Sox11 mutant embryo, RNA was extracted by the RNeasy Plus Micro kit (QIAGEN), and cDNA synthesis and amplification were performed using the cDNA Synthesis and Amplification kit (Affymetrix).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	500ng of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol Rev.3 recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Affymetrix). Double-stranded cDNA was cleaned up by the Sample Cleanup Module (Affymetrix). In vitro transcription was performed on all cDNAs using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin columns (QIAGEN). The cRNA was fragmented by metal-induced hydrolysis.
Sample_hyb_protocol	10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controlled by adding cRNA cocktail (bioB, bioC, bioD, cre). Washing and staining were performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.
Sample_scan_protocol	Scanning was performed in an Affymetrix GeneChip® Scanner 3000 7G. Chip analysis was performed using the Affymetrix GeneChip® Operating Software v1.4.
Sample_data_processing	Affymetrix GeneChip Operating Software v1.4. The average values were scaled to 100 so that all chips could be directly compared.
Sample_platform_id	GPL1261
Sample_contact_name	Sumiko,,Watanabe
Sample_contact_email	sumiko@ims.u-tokyo.ac.jp
Sample_contact_phone	81 3 5449 5663
Sample_contact_fax	81 3 5449 5474
Sample_contact_laboratory	Department of Molecular and Developmentl Bioloty
Sample_contact_department	Institute of Medical Science
Sample_contact_institute	University of Tokyo
Sample_contact_address	4-6-1 Shirokane-dai
Sample_contact_city	Minato-ku, Tokyo
Sample_contact_zip/postal_code	108-8639
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1056nnn/GSM1056321/suppl/GSM1056321_Embryo_Sox11_KO_430.CEL.gz
Sample_series_id	GSE43089
Sample_data_row_count	45101

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