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E-GEOD-13154 - miRNA profiling in male and female chicken embryonic gonads during sexual differentiation

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25 rows


Source Name
GSM329311 1
GSM329312 1
GSM329313 1
GSM329314 1
GSM329315 1
GSM329316 1
GSM329317 1
GSM329318 1
GSM329319 1
GSM329320 1
GSM329321 1
GSM329322 1
GSM329323 1
GSM329324 1
GSM329325 1
GSM329326 1
GSM329327 1
GSM329328 1
GSM329329 1
GSM329330 1
GSM329331 1
GSM329332 1
GSM329333 1
GSM329334 1
GSM329335 1

		Sample Attributes							Variables				Assay
Sample_description	Sample_source_name	exposure	Stage	sexed	Organism	array chip #	Sex	Sexed	STAGE	EXPOSURE	ARRAY CHIP #	SEX	Hybridization Name
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	0.5sec	E5.5 (HH 27-28)	PCR	Gallus gallus	50636	male		E5.5 (HH 27-28)	0.5sec	50636	male	GSM329311
small RNA <200nt	Embryonic gonad	0.2sec	E5.5 (HH 27-28)	PCR	Gallus gallus	50636	male		E5.5 (HH 27-28)	0.2sec	50636	male	GSM329312
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	0.5sec	E5.5 (HH 27-28)	PCR	Gallus gallus	4011845	male		E5.5 (HH 27-28)	0.5sec	4011845	male	GSM329313
small RNA <200nt	Embryonic gonad	2.0sec	E5.5 (HH 27-28)	PCR	Gallus gallus	4011845	male		E5.5 (HH 27-28)	2.0sec	4011845	male	GSM329314
small RNA <200nt	Embryonic gonad	2.0sec	E5.5 (HH 27-28)	PCR	Gallus gallus	4011845	male		E5.5 (HH 27-28)	2.0sec	4011845	male	GSM329315
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	2.0sec	E5.5 (HH 27-28)	PCR	Gallus gallus	50636	female		E5.5 (HH 27-28)	2.0sec	50636	female	GSM329316
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	1.0sec	E5.5 (HH 27-28)	PCR	Gallus gallus	4011845	female		E5.5 (HH 27-28)	1.0sec	4011845	female	GSM329317
small RNA <200nt	Embryonic gonad	2.0sec	E5.5 (HH 27-28)	PCR	Gallus gallus	4011845	female		E5.5 (HH 27-28)	2.0sec	4011845	female	GSM329318
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	2.0sec	E5.5 (HH 27-28)	PCR	Gallus gallus	4011845	female		E5.5 (HH 27-28)	2.0sec	4011845	female	GSM329319
small RNA <200nt	Embryonic gonad	0.2sec	E6.5 (HH 29-30)	PCR	Gallus gallus	50636	male		E6.5 (HH 29-30)	0.2sec	50636	male	GSM329320
0 spots excluded from data extraction	Embryonic gonad	0.1sec	E6.5 (HH 29-30)	PCR	Gallus gallus	50636	male		E6.5 (HH 29-30)	0.1sec	50636	male	GSM329321
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	0.5sec	E6.5 (HH 29-30)	PCR	Gallus gallus	4011845	male		E6.5 (HH 29-30)	0.5sec	4011845	male	GSM329322
small RNA <200nt	Embryonic gonad	1.0sec	E6.5 (HH 29-30)	PCR	Gallus gallus	4011845	male		E6.5 (HH 29-30)	1.0sec	4011845	male	GSM329323
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	1.0sec	E6.5 (HH 29-30)	PCR	Gallus gallus	4011845	male		E6.5 (HH 29-30)	1.0sec	4011845	male	GSM329324
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	0.2sec	E6.5 (HH 29-30)	PCR	Gallus gallus	50636	female		E6.5 (HH 29-30)	0.2sec	50636	female	GSM329325
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	0.1sec	E6.5 (HH 29-30)	PCR	Gallus gallus	50636	female		E6.5 (HH 29-30)	0.1sec	50636	female	GSM329326
small RNA <200nt	Embryonic gonad	1.0sec	E6.5 (HH 29-30)	PCR	Gallus gallus	4011845	female		E6.5 (HH 29-30)	1.0sec	4011845	female	GSM329327
1 spot excluded from data extraction: probe no; 543	Embryonic gonad	1.0sec	E9.5 (HH35-36)		Gallus gallus	4011845	male	Manual	E9.5 (HH35-36)	1.0sec	4011845	male	GSM329328
10 spots excluded from data extraction; 223;268;443;555;973;1056;1128;1176;1187;1323	Embryonic gonad	2.0sec	E9.5 (HH35-36)		Gallus gallus	4011845	male	Manual	E9.5 (HH35-36)	2.0sec	4011845	male	GSM329329
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	2.0sec	E9.5 (HH35-36)		Gallus gallus	4011845	male	Manual	E9.5 (HH35-36)	2.0sec	4011845	male	GSM329330
small RNA <200nt	Embryonic gonad	0.5sec	E9.5 (HH35-36)		Gallus gallus	4011845	male	Manual	E9.5 (HH35-36)	0.5sec	4011845	male	GSM329331
small RNA <200nt	Embryonic gonad	0.5sec	E9.5 (HH35-36)		Gallus gallus	4011845	female	Manual	E9.5 (HH35-36)	0.5sec	4011845	female	GSM329332
small RNA <200nt	Embryonic gonad	2.0sec	E9.5 (HH35-36)		Gallus gallus	4011845	female	Manual	E9.5 (HH35-36)	2.0sec	4011845	female	GSM329333
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	1.0sec	E9.5 (HH35-36)		Gallus gallus	4011845	female	Manual	E9.5 (HH35-36)	1.0sec	4011845	female	GSM329334
small RNA <200nt	Embryonic gonad	1.0sec	E9.5 (HH35-36)		Gallus gallus	4011845	female	Manual	E9.5 (HH35-36)	1.0sec	4011845	female	GSM329335

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E-GEOD-13154 - miRNA profiling in male and female chicken embryonic gonads during sexual differentiation