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Search results for the GEO ID: GSE21749

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Description

Characteristics

GSM542304

GPL1261

Late Spermatocyte, HR6B Knockout, rep1

Testis late spermatocyte, HR6B knockout

background: FVB genotype: Hr6b-/- gender: male age: 4-5 weeks tissue: testis cell type: late spermatocyte

Replicate 1 of 2.

Sample_geo_accession	GSM542304
Sample_status	Public on May 08 2010
Sample_submission_date	May 07 2010
Sample_last_update_date	May 07 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Spermatocytes and round spermatids were isolated from 4-5-week-old Hr6b+/+ and Hr6b-/- mouse testes after collagenase and trypsin treatment, followed by sedimentation at unit gravity (StaPut procedure). Subsequently, cells were further purified by density gradient centrifugation through Percol. Cells were snap-frozen in liquid nitrogen and stored at –80 0C . A sample of each isolated fraction was used for hematoxilin-eosin staining on slides, in order asses the purity of the fractions. The purity of the cells was >80%, and not different between wild type and knockout preparations.
Sample_growth_protocol_ch1	All animal experiments were approved by the animal experiments committee DEC-Consult (EUR 897, EUR1168, EUR 1427). To obtain knockout mice, Hr6b+/- mice, obtained from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to obtain Hr6b-/- females. These were then crossed with Hr6b+/- males derived from backcrosses of Hr6b+/- mice with FVB mice, to yield male Hr6b-/- mice. Hr6b+/+ mice, derived from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to yield male Hr6b+/+ mice. The crosses to obtain male Hr6b+/+ and male Hr6b-/- mice were set up simultaneously, using animals from the same backcross generation (>20).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was prepared from the isolated germ cell preparations by Trizol. The purity, integrity and quality of extracted RNA was measured using Nanodrop and Bioanalyzer 2100 (Agilent technologies).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Affymetrix biotin labeling protocol, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station (Affymetrix hybridization protocol).
Sample_scan_protocol	Signal intensities were generated by scanning arrays using the Affymetrix 7G GeneChip scanner.
Sample_data_processing	RMA normalisation implemented in R /Bioconductor. Linear models and empirical Bayes methods, implemented in Limma (R /Bioconductor), were used to assess differential expression.
Sample_platform_id	GPL1261
Sample_contact_name	Eskeatnaf,,Mulugeta Achame
Sample_contact_email	e.mulugetaachame@erasmusmc.nl
Sample_contact_phone	0031614883537
Sample_contact_laboratory	Reproduction and Development
Sample_contact_department	Reproduction and Development
Sample_contact_institute	Erasmusmc
Sample_contact_address	Dr Molewaterplein 50
Sample_contact_city	Rotterdam
Sample_contact_state	Rotterdam
Sample_contact_zip/postal_code	3015 GE
Sample_contact_country	Netherlands
Sample_contact_web_link	http://www.erasmusmc.nl/rede/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM542nnn/GSM542304/suppl/GSM542304.CEL.gz
Sample_series_id	GSE21749
Sample_data_row_count	45101

GSM542305

GPL1261

Late Spermatocyte, HR6B Knockout, rep2

Testis late spermatocyte, HR6B knockout

background: FVB genotype: Hr6b-/- gender: male age: 4-5 weeks tissue: testis cell type: late spermatocyte

Replicate 2 of 2.

Sample_geo_accession	GSM542305
Sample_status	Public on May 08 2010
Sample_submission_date	May 07 2010
Sample_last_update_date	May 07 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Spermatocytes and round spermatids were isolated from 4-5-week-old Hr6b+/+ and Hr6b-/- mouse testes after collagenase and trypsin treatment, followed by sedimentation at unit gravity (StaPut procedure). Subsequently, cells were further purified by density gradient centrifugation through Percol. Cells were snap-frozen in liquid nitrogen and stored at –80 0C . A sample of each isolated fraction was used for hematoxilin-eosin staining on slides, in order asses the purity of the fractions. The purity of the cells was >80%, and not different between wild type and knockout preparations.
Sample_growth_protocol_ch1	All animal experiments were approved by the animal experiments committee DEC-Consult (EUR 897, EUR1168, EUR 1427). To obtain knockout mice, Hr6b+/- mice, obtained from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to obtain Hr6b-/- females. These were then crossed with Hr6b+/- males derived from backcrosses of Hr6b+/- mice with FVB mice, to yield male Hr6b-/- mice. Hr6b+/+ mice, derived from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to yield male Hr6b+/+ mice. The crosses to obtain male Hr6b+/+ and male Hr6b-/- mice were set up simultaneously, using animals from the same backcross generation (>20).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was prepared from the isolated germ cell preparations by Trizol. The purity, integrity and quality of extracted RNA was measured using Nanodrop and Bioanalyzer 2100 (Agilent technologies).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Affymetrix biotin labeling protocol, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station (Affymetrix hybridization protocol).
Sample_scan_protocol	Signal intensities were generated by scanning arrays using the Affymetrix 7G GeneChip scanner.
Sample_data_processing	RMA normalisation implemented in R /Bioconductor. Linear models and empirical Bayes methods, implemented in Limma (R /Bioconductor), were used to assess differential expression.
Sample_platform_id	GPL1261
Sample_contact_name	Eskeatnaf,,Mulugeta Achame
Sample_contact_email	e.mulugetaachame@erasmusmc.nl
Sample_contact_phone	0031614883537
Sample_contact_laboratory	Reproduction and Development
Sample_contact_department	Reproduction and Development
Sample_contact_institute	Erasmusmc
Sample_contact_address	Dr Molewaterplein 50
Sample_contact_city	Rotterdam
Sample_contact_state	Rotterdam
Sample_contact_zip/postal_code	3015 GE
Sample_contact_country	Netherlands
Sample_contact_web_link	http://www.erasmusmc.nl/rede/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM542nnn/GSM542305/suppl/GSM542305.CEL.gz
Sample_series_id	GSE21749
Sample_data_row_count	45101

GSM542306

GPL1261

Late Spermatocyte, Wildtype, rep1

Testis late spermatocyte, wildtype

background: FVB genotype: Hr6b+/+ gender: male age: 4-5 weeks tissue: testis cell type: late spermatocyte

Replicate 1 of 2.

Sample_geo_accession	GSM542306
Sample_status	Public on May 08 2010
Sample_submission_date	May 07 2010
Sample_last_update_date	May 07 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Spermatocytes and round spermatids were isolated from 4-5-week-old Hr6b+/+ and Hr6b-/- mouse testes after collagenase and trypsin treatment, followed by sedimentation at unit gravity (StaPut procedure). Subsequently, cells were further purified by density gradient centrifugation through Percol. Cells were snap-frozen in liquid nitrogen and stored at –80 0C . A sample of each isolated fraction was used for hematoxilin-eosin staining on slides, in order asses the purity of the fractions. The purity of the cells was >80%, and not different between wild type and knockout preparations.
Sample_growth_protocol_ch1	All animal experiments were approved by the animal experiments committee DEC-Consult (EUR 897, EUR1168, EUR 1427). To obtain knockout mice, Hr6b+/- mice, obtained from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to obtain Hr6b-/- females. These were then crossed with Hr6b+/- males derived from backcrosses of Hr6b+/- mice with FVB mice, to yield male Hr6b-/- mice. Hr6b+/+ mice, derived from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to yield male Hr6b+/+ mice. The crosses to obtain male Hr6b+/+ and male Hr6b-/- mice were set up simultaneously, using animals from the same backcross generation (>20).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was prepared from the isolated germ cell preparations by Trizol. The purity, integrity and quality of extracted RNA was measured using Nanodrop and Bioanalyzer 2100 (Agilent technologies).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Affymetrix biotin labeling protocol, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station (Affymetrix hybridization protocol).
Sample_scan_protocol	Signal intensities were generated by scanning arrays using the Affymetrix 7G GeneChip scanner.
Sample_data_processing	RMA normalisation implemented in R /Bioconductor. Linear models and empirical Bayes methods, implemented in Limma (R /Bioconductor), were used to assess differential expression.
Sample_platform_id	GPL1261
Sample_contact_name	Eskeatnaf,,Mulugeta Achame
Sample_contact_email	e.mulugetaachame@erasmusmc.nl
Sample_contact_phone	0031614883537
Sample_contact_laboratory	Reproduction and Development
Sample_contact_department	Reproduction and Development
Sample_contact_institute	Erasmusmc
Sample_contact_address	Dr Molewaterplein 50
Sample_contact_city	Rotterdam
Sample_contact_state	Rotterdam
Sample_contact_zip/postal_code	3015 GE
Sample_contact_country	Netherlands
Sample_contact_web_link	http://www.erasmusmc.nl/rede/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM542nnn/GSM542306/suppl/GSM542306.CEL.gz
Sample_series_id	GSE21749
Sample_data_row_count	45101

GSM542307

GPL1261

Late Spermatocyte, Wildtype, rep2

Testis late spermatocyte, wildtype

background: FVB genotype: Hr6b+/+ gender: male age: 4-5 weeks tissue: testis cell type: late spermatocyte

Replicate 2 of 2.

Sample_geo_accession	GSM542307
Sample_status	Public on May 08 2010
Sample_submission_date	May 07 2010
Sample_last_update_date	May 07 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Spermatocytes and round spermatids were isolated from 4-5-week-old Hr6b+/+ and Hr6b-/- mouse testes after collagenase and trypsin treatment, followed by sedimentation at unit gravity (StaPut procedure). Subsequently, cells were further purified by density gradient centrifugation through Percol. Cells were snap-frozen in liquid nitrogen and stored at –80 0C . A sample of each isolated fraction was used for hematoxilin-eosin staining on slides, in order asses the purity of the fractions. The purity of the cells was >80%, and not different between wild type and knockout preparations.
Sample_growth_protocol_ch1	All animal experiments were approved by the animal experiments committee DEC-Consult (EUR 897, EUR1168, EUR 1427). To obtain knockout mice, Hr6b+/- mice, obtained from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to obtain Hr6b-/- females. These were then crossed with Hr6b+/- males derived from backcrosses of Hr6b+/- mice with FVB mice, to yield male Hr6b-/- mice. Hr6b+/+ mice, derived from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to yield male Hr6b+/+ mice. The crosses to obtain male Hr6b+/+ and male Hr6b-/- mice were set up simultaneously, using animals from the same backcross generation (>20).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was prepared from the isolated germ cell preparations by Trizol. The purity, integrity and quality of extracted RNA was measured using Nanodrop and Bioanalyzer 2100 (Agilent technologies).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Affymetrix biotin labeling protocol, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station (Affymetrix hybridization protocol).
Sample_scan_protocol	Signal intensities were generated by scanning arrays using the Affymetrix 7G GeneChip scanner.
Sample_data_processing	RMA normalisation implemented in R /Bioconductor. Linear models and empirical Bayes methods, implemented in Limma (R /Bioconductor), were used to assess differential expression.
Sample_platform_id	GPL1261
Sample_contact_name	Eskeatnaf,,Mulugeta Achame
Sample_contact_email	e.mulugetaachame@erasmusmc.nl
Sample_contact_phone	0031614883537
Sample_contact_laboratory	Reproduction and Development
Sample_contact_department	Reproduction and Development
Sample_contact_institute	Erasmusmc
Sample_contact_address	Dr Molewaterplein 50
Sample_contact_city	Rotterdam
Sample_contact_state	Rotterdam
Sample_contact_zip/postal_code	3015 GE
Sample_contact_country	Netherlands
Sample_contact_web_link	http://www.erasmusmc.nl/rede/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM542nnn/GSM542307/suppl/GSM542307.CEL.gz
Sample_series_id	GSE21749
Sample_data_row_count	45101

GSM542308

GPL1261

Round Spermatid, HR6B Knockout, rep1

Testis round spermatid, HR6B knockout

background: FVB genotype: Hr6b-/- gender: male age: 4-5 weeks tissue: testis cell type: round spermatid

Replicate 1 of 2.

Sample_geo_accession	GSM542308
Sample_status	Public on May 08 2010
Sample_submission_date	May 07 2010
Sample_last_update_date	May 07 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Spermatocytes and round spermatids were isolated from 4-5-week-old Hr6b+/+ and Hr6b-/- mouse testes after collagenase and trypsin treatment, followed by sedimentation at unit gravity (StaPut procedure). Subsequently, cells were further purified by density gradient centrifugation through Percol. Cells were snap-frozen in liquid nitrogen and stored at –80 0C . A sample of each isolated fraction was used for hematoxilin-eosin staining on slides, in order asses the purity of the fractions. The purity of the cells was >80%, and not different between wild type and knockout preparations.
Sample_growth_protocol_ch1	All animal experiments were approved by the animal experiments committee DEC-Consult (EUR 897, EUR1168, EUR 1427). To obtain knockout mice, Hr6b+/- mice, obtained from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to obtain Hr6b-/- females. These were then crossed with Hr6b+/- males derived from backcrosses of Hr6b+/- mice with FVB mice, to yield male Hr6b-/- mice. Hr6b+/+ mice, derived from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to yield male Hr6b+/+ mice. The crosses to obtain male Hr6b+/+ and male Hr6b-/- mice were set up simultaneously, using animals from the same backcross generation (>20).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was prepared from the isolated germ cell preparations by Trizol. The purity, integrity and quality of extracted RNA was measured using Nanodrop and Bioanalyzer 2100 (Agilent technologies).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Affymetrix biotin labeling protocol, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station (Affymetrix hybridization protocol).
Sample_scan_protocol	Signal intensities were generated by scanning arrays using the Affymetrix 7G GeneChip scanner.
Sample_data_processing	RMA normalisation implemented in R /Bioconductor. Linear models and empirical Bayes methods, implemented in Limma (R /Bioconductor), were used to assess differential expression.
Sample_platform_id	GPL1261
Sample_contact_name	Eskeatnaf,,Mulugeta Achame
Sample_contact_email	e.mulugetaachame@erasmusmc.nl
Sample_contact_phone	0031614883537
Sample_contact_laboratory	Reproduction and Development
Sample_contact_department	Reproduction and Development
Sample_contact_institute	Erasmusmc
Sample_contact_address	Dr Molewaterplein 50
Sample_contact_city	Rotterdam
Sample_contact_state	Rotterdam
Sample_contact_zip/postal_code	3015 GE
Sample_contact_country	Netherlands
Sample_contact_web_link	http://www.erasmusmc.nl/rede/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM542nnn/GSM542308/suppl/GSM542308.CEL.gz
Sample_series_id	GSE21749
Sample_data_row_count	45101

GSM542309

GPL1261

Round Spermatid, HR6B Knockout, rep2

Testis round spermatid, HR6B knockout

background: FVB genotype: Hr6b-/- gender: male age: 4-5 weeks tissue: testis cell type: round spermatid

Replicate 2 of 2.

Sample_geo_accession	GSM542309
Sample_status	Public on May 08 2010
Sample_submission_date	May 07 2010
Sample_last_update_date	May 07 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Spermatocytes and round spermatids were isolated from 4-5-week-old Hr6b+/+ and Hr6b-/- mouse testes after collagenase and trypsin treatment, followed by sedimentation at unit gravity (StaPut procedure). Subsequently, cells were further purified by density gradient centrifugation through Percol. Cells were snap-frozen in liquid nitrogen and stored at –80 0C . A sample of each isolated fraction was used for hematoxilin-eosin staining on slides, in order asses the purity of the fractions. The purity of the cells was >80%, and not different between wild type and knockout preparations.
Sample_growth_protocol_ch1	All animal experiments were approved by the animal experiments committee DEC-Consult (EUR 897, EUR1168, EUR 1427). To obtain knockout mice, Hr6b+/- mice, obtained from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to obtain Hr6b-/- females. These were then crossed with Hr6b+/- males derived from backcrosses of Hr6b+/- mice with FVB mice, to yield male Hr6b-/- mice. Hr6b+/+ mice, derived from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to yield male Hr6b+/+ mice. The crosses to obtain male Hr6b+/+ and male Hr6b-/- mice were set up simultaneously, using animals from the same backcross generation (>20).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was prepared from the isolated germ cell preparations by Trizol. The purity, integrity and quality of extracted RNA was measured using Nanodrop and Bioanalyzer 2100 (Agilent technologies).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Affymetrix biotin labeling protocol, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station (Affymetrix hybridization protocol).
Sample_scan_protocol	Signal intensities were generated by scanning arrays using the Affymetrix 7G GeneChip scanner.
Sample_data_processing	RMA normalisation implemented in R /Bioconductor. Linear models and empirical Bayes methods, implemented in Limma (R /Bioconductor), were used to assess differential expression.
Sample_platform_id	GPL1261
Sample_contact_name	Eskeatnaf,,Mulugeta Achame
Sample_contact_email	e.mulugetaachame@erasmusmc.nl
Sample_contact_phone	0031614883537
Sample_contact_laboratory	Reproduction and Development
Sample_contact_department	Reproduction and Development
Sample_contact_institute	Erasmusmc
Sample_contact_address	Dr Molewaterplein 50
Sample_contact_city	Rotterdam
Sample_contact_state	Rotterdam
Sample_contact_zip/postal_code	3015 GE
Sample_contact_country	Netherlands
Sample_contact_web_link	http://www.erasmusmc.nl/rede/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM542nnn/GSM542309/suppl/GSM542309.CEL.gz
Sample_series_id	GSE21749
Sample_data_row_count	45101

GSM542310

GPL1261

Round Spermatid, Wildtype, rep1

Testis round spermatid, wildtype

background: FVB genotype: Hr6b+/+ gender: male age: 4-5 weeks tissue: testis cell type: round spermatid

Replicate 1 of 2.

Sample_geo_accession	GSM542310
Sample_status	Public on May 08 2010
Sample_submission_date	May 07 2010
Sample_last_update_date	May 07 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Spermatocytes and round spermatids were isolated from 4-5-week-old Hr6b+/+ and Hr6b-/- mouse testes after collagenase and trypsin treatment, followed by sedimentation at unit gravity (StaPut procedure). Subsequently, cells were further purified by density gradient centrifugation through Percol. Cells were snap-frozen in liquid nitrogen and stored at –80 0C . A sample of each isolated fraction was used for hematoxilin-eosin staining on slides, in order asses the purity of the fractions. The purity of the cells was >80%, and not different between wild type and knockout preparations.
Sample_growth_protocol_ch1	All animal experiments were approved by the animal experiments committee DEC-Consult (EUR 897, EUR1168, EUR 1427). To obtain knockout mice, Hr6b+/- mice, obtained from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to obtain Hr6b-/- females. These were then crossed with Hr6b+/- males derived from backcrosses of Hr6b+/- mice with FVB mice, to yield male Hr6b-/- mice. Hr6b+/+ mice, derived from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to yield male Hr6b+/+ mice. The crosses to obtain male Hr6b+/+ and male Hr6b-/- mice were set up simultaneously, using animals from the same backcross generation (>20).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was prepared from the isolated germ cell preparations by Trizol. The purity, integrity and quality of extracted RNA was measured using Nanodrop and Bioanalyzer 2100 (Agilent technologies).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Affymetrix biotin labeling protocol, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station (Affymetrix hybridization protocol).
Sample_scan_protocol	Signal intensities were generated by scanning arrays using the Affymetrix 7G GeneChip scanner.
Sample_data_processing	RMA normalisation implemented in R /Bioconductor. Linear models and empirical Bayes methods, implemented in Limma (R /Bioconductor), were used to assess differential expression.
Sample_platform_id	GPL1261
Sample_contact_name	Eskeatnaf,,Mulugeta Achame
Sample_contact_email	e.mulugetaachame@erasmusmc.nl
Sample_contact_phone	0031614883537
Sample_contact_laboratory	Reproduction and Development
Sample_contact_department	Reproduction and Development
Sample_contact_institute	Erasmusmc
Sample_contact_address	Dr Molewaterplein 50
Sample_contact_city	Rotterdam
Sample_contact_state	Rotterdam
Sample_contact_zip/postal_code	3015 GE
Sample_contact_country	Netherlands
Sample_contact_web_link	http://www.erasmusmc.nl/rede/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM542nnn/GSM542310/suppl/GSM542310.CEL.gz
Sample_series_id	GSE21749
Sample_data_row_count	45101

GSM542311

GPL1261

Round Spermatid, Wildtype, rep2

Testis round spermatid, wildtype

background: FVB genotype: Hr6b+/+ gender: male age: 4-5 weeks tissue: testis cell type: round spermatid

Replicate 2 of 2.

Sample_geo_accession	GSM542311
Sample_status	Public on May 08 2010
Sample_submission_date	May 07 2010
Sample_last_update_date	May 07 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Spermatocytes and round spermatids were isolated from 4-5-week-old Hr6b+/+ and Hr6b-/- mouse testes after collagenase and trypsin treatment, followed by sedimentation at unit gravity (StaPut procedure). Subsequently, cells were further purified by density gradient centrifugation through Percol. Cells were snap-frozen in liquid nitrogen and stored at –80 0C . A sample of each isolated fraction was used for hematoxilin-eosin staining on slides, in order asses the purity of the fractions. The purity of the cells was >80%, and not different between wild type and knockout preparations.
Sample_growth_protocol_ch1	All animal experiments were approved by the animal experiments committee DEC-Consult (EUR 897, EUR1168, EUR 1427). To obtain knockout mice, Hr6b+/- mice, obtained from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to obtain Hr6b-/- females. These were then crossed with Hr6b+/- males derived from backcrosses of Hr6b+/- mice with FVB mice, to yield male Hr6b-/- mice. Hr6b+/+ mice, derived from backcrosses of Hr6b+/- mice with FVB mice, were intercrossed to yield male Hr6b+/+ mice. The crosses to obtain male Hr6b+/+ and male Hr6b-/- mice were set up simultaneously, using animals from the same backcross generation (>20).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was prepared from the isolated germ cell preparations by Trizol. The purity, integrity and quality of extracted RNA was measured using Nanodrop and Bioanalyzer 2100 (Agilent technologies).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Affymetrix biotin labeling protocol, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station (Affymetrix hybridization protocol).
Sample_scan_protocol	Signal intensities were generated by scanning arrays using the Affymetrix 7G GeneChip scanner.
Sample_data_processing	RMA normalisation implemented in R /Bioconductor. Linear models and empirical Bayes methods, implemented in Limma (R /Bioconductor), were used to assess differential expression.
Sample_platform_id	GPL1261
Sample_contact_name	Eskeatnaf,,Mulugeta Achame
Sample_contact_email	e.mulugetaachame@erasmusmc.nl
Sample_contact_phone	0031614883537
Sample_contact_laboratory	Reproduction and Development
Sample_contact_department	Reproduction and Development
Sample_contact_institute	Erasmusmc
Sample_contact_address	Dr Molewaterplein 50
Sample_contact_city	Rotterdam
Sample_contact_state	Rotterdam
Sample_contact_zip/postal_code	3015 GE
Sample_contact_country	Netherlands
Sample_contact_web_link	http://www.erasmusmc.nl/rede/
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM542nnn/GSM542311/suppl/GSM542311.CEL.gz
Sample_series_id	GSE21749
Sample_data_row_count	45101

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Transcripts profile based on;

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