Source Name Characteristics [exposure] Characteristics [Stage] Characteristics [sexed] Characteristics [Organism] Term Source REF Term Accession Number Characteristics [array chip #] Characteristics [Sex] Term Source REF Term Accession Number Characteristics [Sexed] Comment [Sample_description] Comment [Sample_source_name] Protocol REF Extract Name Material Type Protocol REF Labeled Extract Name Label Material Type Protocol REF Protocol REF Hybridization Name Array Design REF Protocol REF Factor Value [STAGE] Factor Value [EXPOSURE] Factor Value [ARRAY CHIP #] Factor Value [SEX] Term Source REF Term Accession Number Scan Name Array Data File Comment [ArrayExpress FTP file] Protocol REF Derived Array Data File Comment [Derived ArrayExpress FTP file] GSM329313 1 0.5sec E5.5 (HH 27-28) PCR Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 male EFO EFO_0001266 PCR sexing to distinguish male and female embryos was carried out as previously described (Clinton et. al., 2001, Sexing chick embryos: a rapid and simple protocol, Br. Poult. Sci. v42(1), pp 134-138). Small piece of hind-limb tissue was taken from each E5.5 and E6.5 embyo and digested in PCR digestion buffer (50mM KCl; 10mM Tris HCl (pH 8.3); 0.1mg/ml gelatin; 0.45% NP40; 0.45% Tween-20; 200ug/ml Proteinase K) at 55 degrees celcius for minimum of 30 minutes, then 95 degrees celcius for 10 minutes. Digested tissue samples cooled to room temperature. 1ul of digested sample added to each PCR (see paper ref. for reaction mix). RedTaq Polymerase (Sgima) used to amplify products - 1ul/reaction. PCR products routinely run on 1.5-1.8% TBE agarose gel containing GelRed (Biotium). Female positive samples give 2 bands; W-specific band (larger) and 18S control band (smaller). Male positive samples give only 18S control band (no W chromosome in males). Embryonic gonad P-GSE13154-2 GSM329313 extract 1 other P-GSE13154-3 GSM329313 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329313 A-GEOD-7472 P-GSE13154-6 E5.5 (HH 27-28) 0.5sec 4011845 male EFO EFO_0001266 GSM329313.txt GSM329313.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329313_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329324 1 1.0sec E6.5 (HH 29-30) PCR Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 male EFO EFO_0001266 17 spots excluded from data extraction: probe no; 129;278;284;329;417;483;496;662;667;837;889;1003;1059;1122;1182;1196;1354; Embryonic gonad P-GSE13154-2 GSM329324 extract 1 other P-GSE13154-3 GSM329324 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329324 A-GEOD-7472 P-GSE13154-6 E6.5 (HH 29-30) 1.0sec 4011845 male EFO EFO_0001266 GSM329324.txt GSM329324.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329324_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329323 1 1.0sec E6.5 (HH 29-30) PCR Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 male EFO EFO_0001266 small RNA <200nt Embryonic gonad P-GSE13154-2 GSM329323 extract 1 other P-GSE13154-3 GSM329323 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329323 A-GEOD-7472 P-GSE13154-6 E6.5 (HH 29-30) 1.0sec 4011845 male EFO EFO_0001266 GSM329323.txt GSM329323.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329323_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329315 1 2.0sec E5.5 (HH 27-28) PCR Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 male EFO EFO_0001266 small RNA <200nt Embryonic gonad P-GSE13154-2 GSM329315 extract 1 other P-GSE13154-3 GSM329315 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329315 A-GEOD-7472 P-GSE13154-6 E5.5 (HH 27-28) 2.0sec 4011845 male EFO EFO_0001266 GSM329315.txt GSM329315.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329315_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329312 1 0.2sec E5.5 (HH 27-28) PCR Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 50636 male EFO EFO_0001266 small RNA <200nt Embryonic gonad P-GSE13154-2 GSM329312 extract 1 other P-GSE13154-3 GSM329312 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329312 A-GEOD-7472 P-GSE13154-6 E5.5 (HH 27-28) 0.2sec 50636 male EFO EFO_0001266 GSM329312.txt GSM329312.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329312_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329325 1 0.2sec E6.5 (HH 29-30) PCR Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 50636 female EFO EFO_0001265 PCR sexing to distinguish male and female embryos was carried out as previously described (Clinton et. al., 2001, Sexing chick embryos: a rapid and simple protocol, Br. Poult. Sci. v42(1), pp 134-138). Small piece of hind-limb tissue was taken from each E5.5 and E6.5 embyo and digested in PCR digestion buffer (50mM KCl; 10mM Tris HCl (pH 8.3); 0.1mg/ml gelatin; 0.45% NP40; 0.45% Tween-20; 200ug/ml Proteinase K) at 55 degrees celcius for minimum of 30 minutes, then 95 degrees celcius for 10 minutes. Digested tissue samples cooled to room temperature. 1ul of digested sample added to each PCR (see paper ref. for reaction mix). RedTaq Polymerase (Sgima) used to amplify products - 1ul/reaction. PCR products routinely run on 1.5-1.8% TBE agarose gel containing GelRed (Biotium). Female positive samples give 2 bands; W-specific band (larger) and 18S control band (smaller). Male positive samples give only 18S control band (no W chromosome in males). Embryonic gonad P-GSE13154-2 GSM329325 extract 1 other P-GSE13154-3 GSM329325 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329325 A-GEOD-7472 P-GSE13154-6 E6.5 (HH 29-30) 0.2sec 50636 female EFO EFO_0001265 GSM329325.txt GSM329325.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329325_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329320 1 0.2sec E6.5 (HH 29-30) PCR Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 50636 male EFO EFO_0001266 small RNA <200nt Embryonic gonad P-GSE13154-2 GSM329320 extract 1 other P-GSE13154-3 GSM329320 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329320 A-GEOD-7472 P-GSE13154-6 E6.5 (HH 29-30) 0.2sec 50636 male EFO EFO_0001266 GSM329320.txt GSM329320.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329320_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329317 1 1.0sec E5.5 (HH 27-28) PCR Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 female EFO EFO_0001265 Gonads were dissected from chicken embryos at embryonic days 5.5, 6.5 and 9.5 in PBS treated with diethylpyrocarbonate (DEPC). Gonad pairs from individual E5.5 and E6.5 embryos were lysed in 30ul of miRNA lysis/binding buffer (Ambion mirVana miRNA isolation kit), vortexed and incubated at 4 degrees celcius until sexing was carried out. Then, gonad lysates were pooled by sex for miRNA extraction. E9.5 embryos were sexed manually during dissection given asymmetric development of female gonads can be used to visually distinguish male and female embryos. E9.5 gonads were pooled directly by sex during dissection, into 300ul of miRNA lysis/binding buffer on ice/4 degrees celcius until miRNA extraction. Embryonic gonad P-GSE13154-2 GSM329317 extract 1 other P-GSE13154-3 GSM329317 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329317 A-GEOD-7472 P-GSE13154-6 E5.5 (HH 27-28) 1.0sec 4011845 female EFO EFO_0001265 GSM329317.txt GSM329317.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329317_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329330 1 2.0sec E9.5 (HH35-36) Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 male EFO EFO_0001266 Manual Gonads were dissected from chicken embryos at embryonic days 5.5, 6.5 and 9.5 in PBS treated with diethylpyrocarbonate (DEPC). Gonad pairs from individual E5.5 and E6.5 embryos were lysed in 30ul of miRNA lysis/binding buffer (Ambion mirVana miRNA isolation kit), vortexed and incubated at 4 degrees celcius until sexing was carried out. Then, gonad lysates were pooled by sex for miRNA extraction. E9.5 embryos were sexed manually during dissection given asymmetric development of female gonads can be used to visually distinguish male and female embryos. E9.5 gonads were pooled directly by sex during dissection, into 300ul of miRNA lysis/binding buffer on ice/4 degrees celcius until miRNA extraction. Embryonic gonad P-GSE13154-2 GSM329330 extract 1 other P-GSE13154-3 GSM329330 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329330 A-GEOD-7472 P-GSE13154-6 E9.5 (HH35-36) 2.0sec 4011845 male EFO EFO_0001266 GSM329330.txt GSM329330.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329330_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329314 1 2.0sec E5.5 (HH 27-28) PCR Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 male EFO EFO_0001266 small RNA <200nt Embryonic gonad P-GSE13154-2 GSM329314 extract 1 other P-GSE13154-3 GSM329314 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329314 A-GEOD-7472 P-GSE13154-6 E5.5 (HH 27-28) 2.0sec 4011845 male EFO EFO_0001266 GSM329314.txt GSM329314.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329314_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329328 1 1.0sec E9.5 (HH35-36) Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 male EFO EFO_0001266 Manual 1 spot excluded from data extraction: probe no; 543 Embryonic gonad P-GSE13154-2 GSM329328 extract 1 other P-GSE13154-3 GSM329328 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329328 A-GEOD-7472 P-GSE13154-6 E9.5 (HH35-36) 1.0sec 4011845 male EFO EFO_0001266 GSM329328.txt GSM329328.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329328_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329334 1 1.0sec E9.5 (HH35-36) Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 female EFO EFO_0001265 Manual PCR sexing to distinguish male and female embryos was carried out as previously described (Clinton et. al., 2001, Sexing chick embryos: a rapid and simple protocol, Br. Poult. Sci. v42(1), pp 134-138). Small piece of hind-limb tissue was taken from each E5.5 and E6.5 embyo and digested in PCR digestion buffer (50mM KCl; 10mM Tris HCl (pH 8.3); 0.1mg/ml gelatin; 0.45% NP40; 0.45% Tween-20; 200ug/ml Proteinase K) at 55 degrees celcius for minimum of 30 minutes, then 95 degrees celcius for 10 minutes. Digested tissue samples cooled to room temperature. 1ul of digested sample added to each PCR (see paper ref. for reaction mix). RedTaq Polymerase (Sgima) used to amplify products - 1ul/reaction. PCR products routinely run on 1.5-1.8% TBE agarose gel containing GelRed (Biotium). Female positive samples give 2 bands; W-specific band (larger) and 18S control band (smaller). Male positive samples give only 18S control band (no W chromosome in males). Embryonic gonad P-GSE13154-2 GSM329334 extract 1 other P-GSE13154-3 GSM329334 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329334 A-GEOD-7472 P-GSE13154-6 E9.5 (HH35-36) 1.0sec 4011845 female EFO EFO_0001265 GSM329334.txt GSM329334.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329334_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329335 1 1.0sec E9.5 (HH35-36) Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 female EFO EFO_0001265 Manual small RNA <200nt Embryonic gonad P-GSE13154-2 GSM329335 extract 1 other P-GSE13154-3 GSM329335 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329335 A-GEOD-7472 P-GSE13154-6 E9.5 (HH35-36) 1.0sec 4011845 female EFO EFO_0001265 GSM329335.txt GSM329335.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329335_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329329 1 2.0sec E9.5 (HH35-36) Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 male EFO EFO_0001266 Manual 10 spots excluded from data extraction; 223;268;443;555;973;1056;1128;1176;1187;1323 Embryonic gonad P-GSE13154-2 GSM329329 extract 1 other P-GSE13154-3 GSM329329 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329329 A-GEOD-7472 P-GSE13154-6 E9.5 (HH35-36) 2.0sec 4011845 male EFO EFO_0001266 GSM329329.txt GSM329329.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329329_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329318 1 2.0sec E5.5 (HH 27-28) PCR Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 female EFO EFO_0001265 small RNA <200nt Embryonic gonad P-GSE13154-2 GSM329318 extract 1 other P-GSE13154-3 GSM329318 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329318 A-GEOD-7472 P-GSE13154-6 E5.5 (HH 27-28) 2.0sec 4011845 female EFO EFO_0001265 GSM329318.txt GSM329318.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329318_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329326 1 0.1sec E6.5 (HH 29-30) PCR Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 50636 female EFO EFO_0001265 Gonads were dissected from chicken embryos at embryonic days 5.5, 6.5 and 9.5 in PBS treated with diethylpyrocarbonate (DEPC). Gonad pairs from individual E5.5 and E6.5 embryos were lysed in 30ul of miRNA lysis/binding buffer (Ambion mirVana miRNA isolation kit), vortexed and incubated at 4 degrees celcius until sexing was carried out. Then, gonad lysates were pooled by sex for miRNA extraction. E9.5 embryos were sexed manually during dissection given asymmetric development of female gonads can be used to visually distinguish male and female embryos. E9.5 gonads were pooled directly by sex during dissection, into 300ul of miRNA lysis/binding buffer on ice/4 degrees celcius until miRNA extraction. Embryonic gonad P-GSE13154-2 GSM329326 extract 1 other P-GSE13154-3 GSM329326 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329326 A-GEOD-7472 P-GSE13154-6 E6.5 (HH 29-30) 0.1sec 50636 female EFO EFO_0001265 GSM329326.txt GSM329326.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329326_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329332 1 0.5sec E9.5 (HH35-36) Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 female EFO EFO_0001265 Manual small RNA <200nt Embryonic gonad P-GSE13154-2 GSM329332 extract 1 other P-GSE13154-3 GSM329332 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329332 A-GEOD-7472 P-GSE13154-6 E9.5 (HH35-36) 0.5sec 4011845 female EFO EFO_0001265 GSM329332.txt GSM329332.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329332_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329316 1 2.0sec E5.5 (HH 27-28) PCR Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 50636 female EFO EFO_0001265 Gonads were dissected from chicken embryos at embryonic days 5.5, 6.5 and 9.5 in PBS treated with diethylpyrocarbonate (DEPC). Gonad pairs from individual E5.5 and E6.5 embryos were lysed in 30ul of miRNA lysis/binding buffer (Ambion mirVana miRNA isolation kit), vortexed and incubated at 4 degrees celcius until sexing was carried out. Then, gonad lysates were pooled by sex for miRNA extraction. E9.5 embryos were sexed manually during dissection given asymmetric development of female gonads can be used to visually distinguish male and female embryos. E9.5 gonads were pooled directly by sex during dissection, into 300ul of miRNA lysis/binding buffer on ice/4 degrees celcius until miRNA extraction. Embryonic gonad P-GSE13154-2 GSM329316 extract 1 other P-GSE13154-3 GSM329316 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329316 A-GEOD-7472 P-GSE13154-6 E5.5 (HH 27-28) 2.0sec 50636 female EFO EFO_0001265 GSM329316.txt GSM329316.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329316_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329331 1 0.5sec E9.5 (HH35-36) Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 male EFO EFO_0001266 Manual small RNA <200nt Embryonic gonad P-GSE13154-2 GSM329331 extract 1 other P-GSE13154-3 GSM329331 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329331 A-GEOD-7472 P-GSE13154-6 E9.5 (HH35-36) 0.5sec 4011845 male EFO EFO_0001266 GSM329331.txt GSM329331.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329331_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329327 1 1.0sec E6.5 (HH 29-30) PCR Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 female EFO EFO_0001265 small RNA <200nt Embryonic gonad P-GSE13154-2 GSM329327 extract 1 other P-GSE13154-3 GSM329327 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329327 A-GEOD-7472 P-GSE13154-6 E6.5 (HH 29-30) 1.0sec 4011845 female EFO EFO_0001265 GSM329327.txt GSM329327.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329327_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329321 1 0.1sec E6.5 (HH 29-30) PCR Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 50636 male EFO EFO_0001266 0 spots excluded from data extraction Embryonic gonad P-GSE13154-2 GSM329321 extract 1 other P-GSE13154-3 GSM329321 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329321 A-GEOD-7472 P-GSE13154-6 E6.5 (HH 29-30) 0.1sec 50636 male EFO EFO_0001266 GSM329321.txt GSM329321.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329321_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329311 1 0.5sec E5.5 (HH 27-28) PCR Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 50636 male EFO EFO_0001266 PCR sexing to distinguish male and female embryos was carried out as previously described (Clinton et. al., 2001, Sexing chick embryos: a rapid and simple protocol, Br. Poult. Sci. v42(1), pp 134-138). Small piece of hind-limb tissue was taken from each E5.5 and E6.5 embyo and digested in PCR digestion buffer (50mM KCl; 10mM Tris HCl (pH 8.3); 0.1mg/ml gelatin; 0.45% NP40; 0.45% Tween-20; 200ug/ml Proteinase K) at 55 degrees celcius for minimum of 30 minutes, then 95 degrees celcius for 10 minutes. Digested tissue samples cooled to room temperature. 1ul of digested sample added to each PCR (see paper ref. for reaction mix). RedTaq Polymerase (Sgima) used to amplify products - 1ul/reaction. PCR products routinely run on 1.5-1.8% TBE agarose gel containing GelRed (Biotium). Female positive samples give 2 bands; W-specific band (larger) and 18S control band (smaller). Male positive samples give only 18S control band (no W chromosome in males). Embryonic gonad P-GSE13154-2 GSM329311 extract 1 other P-GSE13154-3 GSM329311 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329311 A-GEOD-7472 P-GSE13154-6 E5.5 (HH 27-28) 0.5sec 50636 male EFO EFO_0001266 GSM329311.txt GSM329311.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329311_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329322 1 0.5sec E6.5 (HH 29-30) PCR Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 male EFO EFO_0001266 PCR sexing to distinguish male and female embryos was carried out as previously described (Clinton et. al., 2001, Sexing chick embryos: a rapid and simple protocol, Br. Poult. Sci. v42(1), pp 134-138). Small piece of hind-limb tissue was taken from each E5.5 and E6.5 embyo and digested in PCR digestion buffer (50mM KCl; 10mM Tris HCl (pH 8.3); 0.1mg/ml gelatin; 0.45% NP40; 0.45% Tween-20; 200ug/ml Proteinase K) at 55 degrees celcius for minimum of 30 minutes, then 95 degrees celcius for 10 minutes. Digested tissue samples cooled to room temperature. 1ul of digested sample added to each PCR (see paper ref. for reaction mix). RedTaq Polymerase (Sgima) used to amplify products - 1ul/reaction. PCR products routinely run on 1.5-1.8% TBE agarose gel containing GelRed (Biotium). Female positive samples give 2 bands; W-specific band (larger) and 18S control band (smaller). Male positive samples give only 18S control band (no W chromosome in males). Embryonic gonad P-GSE13154-2 GSM329322 extract 1 other P-GSE13154-3 GSM329322 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329322 A-GEOD-7472 P-GSE13154-6 E6.5 (HH 29-30) 0.5sec 4011845 male EFO EFO_0001266 GSM329322.txt GSM329322.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329322_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329319 1 2.0sec E5.5 (HH 27-28) PCR Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 female EFO EFO_0001265 PCR sexing to distinguish male and female embryos was carried out as previously described (Clinton et. al., 2001, Sexing chick embryos: a rapid and simple protocol, Br. Poult. Sci. v42(1), pp 134-138). Small piece of hind-limb tissue was taken from each E5.5 and E6.5 embyo and digested in PCR digestion buffer (50mM KCl; 10mM Tris HCl (pH 8.3); 0.1mg/ml gelatin; 0.45% NP40; 0.45% Tween-20; 200ug/ml Proteinase K) at 55 degrees celcius for minimum of 30 minutes, then 95 degrees celcius for 10 minutes. Digested tissue samples cooled to room temperature. 1ul of digested sample added to each PCR (see paper ref. for reaction mix). RedTaq Polymerase (Sgima) used to amplify products - 1ul/reaction. PCR products routinely run on 1.5-1.8% TBE agarose gel containing GelRed (Biotium). Female positive samples give 2 bands; W-specific band (larger) and 18S control band (smaller). Male positive samples give only 18S control band (no W chromosome in males). Embryonic gonad P-GSE13154-2 GSM329319 extract 1 other P-GSE13154-3 GSM329319 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329319 A-GEOD-7472 P-GSE13154-6 E5.5 (HH 27-28) 2.0sec 4011845 female EFO EFO_0001265 GSM329319.txt GSM329319.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329319_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip GSM329333 1 2.0sec E9.5 (HH35-36) Gallus gallus EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_9031 4011845 female EFO EFO_0001265 Manual small RNA <200nt Embryonic gonad P-GSE13154-2 GSM329333 extract 1 other P-GSE13154-3 GSM329333 LE 1 ULS-Cy5 unknown P-GSE13154-4 P-GSE13154-5 GSM329333 A-GEOD-7472 P-GSE13154-6 E9.5 (HH35-36) 2.0sec 4011845 female EFO EFO_0001265 GSM329333.txt GSM329333.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.raw.1.zip P-GSE13154-1 GSM329333_sample_table.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-13154/E-GEOD-13154.processed.1.zip