imported>Ctelmer: /* QPCR and Nanostring Data Relevant to Ectoderm Network */

2020-04-14T18:31:08Z

QPCR and Nanostring Data Relevant to Ectoderm Network

← Older revision		Revision as of 18:31, 14 April 2020
Line 1:		Line 1:
	= QPCR and Nanostring Data Relevant to Ectoderm Network =		= QPCR and Nanostring Data Relevant to Ectoderm Network =
			<p>Note that the gene names listed in the table have been updated according to nomenclature guidelines and may have changed on the gene pages in Echinobase, however, they are listed as synonyms and the gene pages can be found by searching for the name listed in the table.</p>

	== Perturbation Ct:[Ub-C]-[Ub-Exp] ==		== Perturbation Ct:[Ub-C]-[Ub-Exp] ==

imported>BArsh: /* March 01, 2010 */

2020-03-27T02:01:38Z

March 01, 2010

← Older revision		Revision as of 02:01, 27 March 2020
Line 13,866:		Line 13,866:

	\|}		\|}


			'''Note:''' Smaller effects are shown as "NS", except where individual NS data are included together with other significant measurements to display scatter or inconsistencies amongst different batches of cDNA. Commas separate replicate measurements in the same cDNA batch; slashes indicate different batches of cDNA from independent experiments, dashes indicate a missing data point

			==Perturbation==

			{\|
			\|width="50%"\| '''Perturbation:'''
			\|width="50%"\| '''Genes not affected or shown to be affected only indirectly (8 to 30h, unless otherwise noted)'''
			\|-
			\| '''BMP2/4 MASO<sup>7</sup>'''
			\| ''[atbf1, bra, chordin, dri, e2f3, foxa, foxj1, foxk, gsc, hes, hesc, hlf, hmx, hnf6, lefty, lim1, mitf, nfe2, nodal, otxb1/2, shr2, soxb1, soxc, tead4, vegf3 (18-24 h)], [arnt, ets4, hmg2, myb, myc, pax2/5/8, pea3, runt, six3, z173, z188, z199, z487, z55, z60, z85, z86, z92 (24 h)]''
			\|-
			\| '''Bra MASO<sup>4</sup>'''
			\| ''[bmp2/4, bra, chordin, foxa, foxj1, foxk, fxr/ecr, hes, hesc, hlf, hmx, hnf6, lefty, lim1, nfe2, nk2.2, nodal, otxb1/2, shr2, sip1, soxb1, soxc, tbx2/3, tead4, vegf3 (24-30 h)]''
			\|-
			\| '''Chordin MASO<sup>7</sup>'''
			\| ''[atbf1, bmp2/4, chordin, dri, e2f3, foxa, foxj1, foxk, hes, hesc, hlf, hmx, hnf6, lefty, lim1, mitf, nfe2, nk2.2, nodal, otxb1/2, shr2, sip1, soxb1, soxc, tead4, vegf3 (18-24 h)], [arnt, ets4, hmg2, hox7, msx, myb, myc, pax2/5/8, pea3, runt, six3, z173, z188, z199, z487, z55, z60, z85, z86, z92 (24 h)]''
			\|-
			\| '''Dlx MASO<sup>7</sup>'''
			\| ''[atbf1, bmp2/4, bra, chordin, dri, e2f3, foxj1, foxk, fxr/ecr, hes, hesc, hnf6, lefty, lim1, mitf, nfe2, nk2.2, nodal, shr2, soxb1, soxc, tead4, vegf3 (18-24 h)], [hox7, msx (24 h)]''
			\|-
			\| '''Dri MASO<sup>5</sup>'''
			\| ''bra (24-32 h), gcm (28-48 h), [bmp2/4, foxk, fxr/ecr, hesc, hlf, shr2, sip1, tead4 (24-30 h)], [decorin, fvmo, pks (30-48 h)], [e(s), elk, eve, foxb, gatac, gatae, hox11/13b, lim1, not, notch, nrl, otx, su(h), wnt8 (28-32 h)]''
			\|-
			\| '''Ecr MASO<sup>7</sup>'''
			\| ''[atbf1, bmp2/4, bra, chordin, dlx, dri, e2f3, foxa, foxg, foxj1, foxk, fxr/ecr, gsc, hes, hesc, hlf, hmx, hnf6, irxa, lefty, lhx2.9, lim1, mitf, nfe2, nk1, nk2.2, nodal, otxb1/2, shr2, sip1, soxb1, soxc, tbx2/3, tead4, vegf3 (18-24 h)], [arnt, ets4, hmg2, hox7, msx, myb, myc, pax2/5/8, pea3, runt, six3, z173, z188, z199, z487, z55, z60, z85, z86, z92 (24 h)]''
			\|-
			\| '''FoxA MASO<sup>4</sup>'''
			\| ''[atbf1, bmp2/4, bra, chordin, dlx, e2f3, foxa, foxg, foxj1, foxk, fxr/ecr, gsc, hes, hesc, hlf, hmx, hnf6, irxa, lefty, lhx2.9, lim1, nfe2, nk1, nk2.2, nodal, otxb1/2, shr2, sip1, soxb1, soxc, tbx2/3, tead4, vegf3 (24-30 h)]''
			\|-
			\| '''FoxG MASO<sup>7</sup>'''
			\| ''[bmp2/4, bra, foxj1, foxk, hes, hesc, hlf, lim1, nfe2, nodal, otxb1/2, shr2, soxb1, tead4 (18-24 h)], [arnt, hmg2, myb, myc, pax2/5/8, runt, sip1, z173, z188, z199, z60, z85, z92 (24 h)]''
			\|-
			\| '''FoxJ1 MASO<sup>4</sup>'''
			\| ''[atbf1, bmp2/4, bra, chordin, dri, e2f3, foxa, foxk, fxr/ecr, hes, hesc, hlf, hmx, hnf6, lefty, lhx2.9, lim1, mitf, nfe2, nodal, otxb1/2, shr2, sip1, soxb1, soxc, tead4, vegf3 (18-24 h)]''
			\|-
			\| '''FoxK MASO<sup>4</sup>'''
			\| ''[bra, dri, e2f3, foxj1, foxk, hesc, hnf6, nfe2, shr2, soxc, tead4, vegf3 (18-24 h)]''
			\|-
			\| '''Gsc MASO<sup>7</sup>'''
			\| ''[chordin, foxk, hesc, lefty, nfe2, nodal, shr2, soxb1, tead4 (18-24 h)], [coup-tf1, hmg2, myb, pax2/5/8, z173, z188, z487, z60, z85, z92 (24 h)]''
			\|-
			\| '''HesC MASO<sup>4</sup>'''
			\| ''[e2f3, foxk, hes, nfe2, shr2, sip1, soxc (18-24 h)]''
			\|-
			\| '''Hlf MASO<sup>8</sup>'''
			\| ''[arnt, ets4, hmg2, lefty, myb, nk2.2, nodal, tbx2/3, z173, z487, z60, z85, z92 (24 h)]''
			\|-
			\| '''Hmx MASO<sup>7</sup>'''
			\| ''[atbf1, bmp2/4, bra, chordin, dlx, e2f3, foxa, foxg, foxj1, foxk, fxr/ecr, gsc, hes, hesc, hlf, hnf6, irxa, lefty, lhx2.9, lim1, mitf, nfe2, nk1, nk2.2, nodal, otxb1/2, shr2, sip1, soxb1, soxc, tbx2/3, tead4, vegf3 (18-24 h)], [arnt, ets4, hmg2, hox7, msx, myb, myc, pax2/5/8, pea3, runt, six3, z173, z188, z199, z487, z55, z60, z85, z86, z92 (24 h)]''
			\|-
			\| '''Hnf6 MASO<sup>2,9</sup>'''
			\| ''[foxj1, foxk, hes, hesc, lim1, nfe2, otxb1/2, shr2, soxb1, soxc, tead4 (24-30 h)], [arnt, ets4, hmg2, myb, myc, pax2/5/8, pea3, runt, six3, z173, z188, z199, z487, z60, z92 (24 h)], [eve, foxb, gatac, gcm, lim1, msp130, otx1/2, sm50, spec1 (30, 48 h)]''
			\|-
			\| '''Hox7 MASO<sup>8</sup>'''
			\| ''[hes, hesc, hnf6, mitf, myb, myc, nfe2, shr2, sip1, soxc, vegf3, z173, z188, z199, z487, z60, z92 (24 h)]''
			\|-
			\| '''IrxA MASO<sup>7</sup>'''
			\| ''[dri, hes, nfe2, shr2, soxb1, tead4 (18-24 h)], [arnt, ets4, myb, myc, pax2/5/8, runt, sip1, z173, z487, z60, z92 (24 h)]''
			\|-
			\| '''Lefty MASO<sup>7</sup>'''
			\| ''[atbf1, bra, dri, e2f3, foxa, foxj1, foxk, hes, hesc, hlf, hnf6, lim1, nfe2, otxb1/2, shr2, sip1, soxb1, soxc, tead4, vegf3 (18-24 h)], [arnt, ets4, hmg2, hox7, myb, myc, pax2/5/8, pea3, runt, six3, z173, z188, z199, z487, z55, z60, z85, z86, z92 (24 h)]''
			\|-
			\| '''Lhx2.9 MASO<sup>4</sup>'''
			\| ''[atbf1, bmp2/4, bra, chordin, dlx, e2f3, foxj1, foxk, fxr/ecr, hesc, hmx, hnf6, lefty, lim1, mitf, nfe2, nk2.2, nodal, otxb1/2, shr2, sip1, soxb1, soxc, tbx2/3, tead4, vegf3 (24-30 h)]''
			\|-
			\| '''Lim1 MASO<sup>7</sup>'''
			\| ''[atbf1, bra, chordin, dri, e2f3, foxa, foxj1, foxk, fxr/ecr, hesc, hlf, hmx, hnf6, lefty, mitf, nfe2, nk2.2, nodal, otxb1/2, shr2, sip1, soxb1, soxc, tead4 (18-24 h)], [arnt, ets4, hmg2, hox7, msx, myb, myc, pax2/5/8, pea3, runt, six3, z173, z188, z199, z487, z55, z60, z85, z86, z92 (24 h)]''
			\|-
			\| '''NK1 MASO<sup>7</sup>'''
			\| ''[bmp2/4, bra, dri, foxj1, foxk, fxr/ecr, hesc, hlf, hnf6, lim1, nfe2, nodal, otxb1/2, shr2, soxb1, soxc, tead4 (24-30 h)], [arnt, ets4, foxa, hmg2, myb, myc, pax2/5/8, pea3, runt, z173, z199, z487, z60, z86, z92 (24 h)]''
			\|-
			\| '''NK2.2 MASO<sup>7</sup>'''
			\| ''[atbf1, bmp2/4, bra, chordin, dlx, dri, e2f3, foxa, foxg, foxj1, foxk, gsc, hes, hesc, hlf, hmx, hnf6, lefty, lhx2.9, lim1, mitf, nfe2, nodal, otxb1/2, shr2, sip1, soxb1, soxc, tbx2/3, tead4, vegf3 (18-24 h)], [hox7, msx (24 h)]''
			\|-
			\| '''Nodal MASO<sup>6</sup>'''
			\| ''atbf1, e2f3, ecr (12-30 h), foxj1, foxk, foxl1, hes, hlf, hnf6, mitf, nfe2, nk2.1, shr2, smad3, smad4, soxC, tead4, zfhox1, [bra, foxa, fxr/ecr, hesc, hmx, sip1, soxb1 (18-24 h)]''
			\|-
			\| '''Nodal MOE<sup>1</sup>'''
			\| ''atbf1, dri, e2f3, ecr, foxk, foxl1, gsc, hes, hlf, hnf6, lhx2.9, mitf, nfe2, nk2.1, shr2, smad3, smad4, soxC, tead4, zfhox1''
			\|-
			\| '''Otxb MASO<sup>7</sup>'''
			\| ''[atbf1, bmp2/4, bra, chordin, dlx, e2f3, foxa, foxj1, foxk, fxr/ecr, hesc, hmx, hnf6, lefty, lhx2.9, lim1, nfe2, nk2.2, nodal, otxb1/2, shr2, sip1, soxb1, soxc, tbx2/3, tead4, vegf3 (24-30 h)], [arnt, ets4, hmg2, hox7, msx, myb, myc, pax2/5/8, pea3, runt, six3, z173, z188, z199, z487, z55, z60, z85, z86, z92 (24 h)]''
			\|-
			\| '''Sip1 MASO<sup>7</sup>'''
			\| ''[bmp2/4, dri, e2f3, foxj1, foxk, fxr/ecr, hesc, hlf, hmx, hnf6, lim1, nfe2, nodal, shr2, soxb1, soxc, tead4 (18-24 h)], [ets4, hmg2, hox7 (24 h)]''
			\|-
			\| '''SoxC MASO<sup>7</sup>'''
			\| ''foxa (18-24 h), [atbf1, bmp2/4, bra, chordin, dri, e2f3, foxj1, foxk, fxr/ecr, hes, hesc, hlf, hmx, hnf6, lhx2.9, lim1, mitf, nfe2, nodal, otxb1/2, shr2, sip1, soxb1, tead4, vegf3 (18-30 h)], [arnt, ets4, hmg2, hox7, msx, myb, myc, pax2/5/8, pea3, runt, six3, z173, z188, z199, z487, z55, z60, z85, z86, z92 (24 h)]''
			\|-
			\| '''Tbx2/3 MASO<sup>7</sup>'''
			\| ''[dri, hesc, shr2, soxc, tead4 (18-24 h)], [arnt, sip1, z92 (24 h)]''
			\|}

			=== Footnotes ===

			<sup>*</sup>Nanostring data: displayed DeltaCt converted from fold change data

			<sup>1</sup>Data of J. Nam

			<sup>2</sup>MASO against both long and short forms of Hnf6 mRNA included in this table

			<sup>4</sup>Data of Y.H. Su

			<sup>5</sup>Data of G. Amore, Y.H. Su

			<sup>6</sup>Data of J. Nam, Y.H. Su

			<sup>7</sup>Data of Y.H. Su, E. Li

			<sup>8</sup>Data of E. Li

			<sup>9</sup>Data from E. Li and other sources

imported>BArsh at 01:58, 27 March 2020

2020-03-27T01:58:16Z

← Older revision		Revision as of 01:58, 27 March 2020
Line 1:		Line 1:
			= QPCR and Nanostring Data Relevant to Ectoderm Network =

			== Perturbation Ct:[Ub-C]-[Ub-Exp] ==

			== March 01, 2010 ==

			Ub, ubiquitin mRNA control used for internal standardization; C<sub>T</sub>, cycle no. at threshold; C, control embryo sample; Exp, sample from perturbed embryos. The quantity of transcript at any point in the reaction is I(1.94<sup>C<sub>T</sub></sup>), where I is the initial amount in the reaction mixture. A positive number means the number of transcripts is increased by the perturbation; a negative number means the number of transcripts is decreased. Data are listed that are considered significant where significant means more than three-fold increase or decrease from control transcript levels (normalized C<sub>T</sub> difference from control is <-1.6 or >+1.6). Smaller effects are shown as "NS", except where individual NS data are included together with other significant measurements to display scatter or inconsistencies amongst different batches of cDNA. Commas separate replicate measurements in the same cDNA batch; slashes indicate different batches of cDNA from independent experiments.

			'''NOTE:''' Nanostring results are mixed with QPCR results in the table. Nanostring values, noted in the table with (*), were converted from fold change to DeltaCt for direct comparison with QPCR results.

	{\| style="border:solid 1px black" class="sortable"		{\| style="border:solid 1px black" class="sortable"
	!Gene!!Perturbation!!12-16 h!!17-21 h!!23-28 h!!30-36 h!!41-48 h!!60-72 h!!Data of:		!Gene!!Perturbation!!12-16 h!!17-21 h!!23-28 h!!30-36 h!!41-48 h!!60-72 h!!Data of:

imported>BArsh: Created page with "{| style="border:solid 1px black" class="sortable" !Gene!!Perturbation!!12-16 h!!17-21 h!!23-28 h!!30-36 h!!41-48 h!!60-72 h!!Data of: |- | rowspan="19" width="77" | '''''alx..."

2020-03-27T01:50:53Z

Created page with "{| style="border:solid 1px black" class="sortable" !Gene!!Perturbation!!12-16 h!!17-21 h!!23-28 h!!30-36 h!!41-48 h!!60-72 h!!Data of: |- | rowspan="19" width="77" | '''''alx..."

Show changes

EctoQPCRandNano - Revision history

imported>Ctelmer: /* QPCR and Nanostring Data Relevant to Ectoderm Network */

imported>BArsh: /* March 01, 2010 */

imported>BArsh at 01:58, 27 March 2020

imported>BArsh: Created page with "{| style="border:solid 1px black" class="sortable" !Gene!!Perturbation!!12-16 h!!17-21 h!!23-28 h!!30-36 h!!41-48 h!!60-72 h!!Data of: |- | rowspan="19" width="77" | '''''alx..."