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==Samples== ===Dr. Yi Zhang lab=== ====Wt mouse samples received on May 2011==== # Sperms: ~50cell/tube; 15 tubes # ES cells: ~50cell/tube; 15 tubes # E9.5 bag: ~641 cells in 1 tube; ~316 cells in 1 tube. # E11.5 bag: ~21550 cells in 1 tube. # E13.5 bag: ~30078 cells in 1 tube (male PGCs); ~57059 cells in 1 tube (female PGCs) ====PGC samples==== Samples for Tn5mCseq (2 sets) {| {{table}} border=1 | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''1st shipped samples''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''2nd shipped samples''' |- | ||||cell # in tube||Used cells||Hiseq||Left cells||||cells |- | Female/Wt/Somatic||1||17,366||4,342||Indx73||0||1||11,064 |- | ||2||7,812||3,906||Indx74||3,906||2||17,848 |- | Female/Wt/PGC||1||3,728||3,728||Indx75||0||1||5,251 |- | ||2||1,575||1,575||Indx76||0||2||3,766 |- | Female/homo/Somatic||1||17,163||4,291||Indx77||12,872||1||15,200 |- | ||2||25,522||4,254||Indx78||21,268||2||14,917 |- | Female/homo/PGC||1||6,531||3,266||Indx79||3,266||1||1,400 |- | ||2||4,700||4,700||Indx80||0||2||1,860 |} 1. Determine exactly what is demethylated in male pronucleus in zygotes. For this project, we need to do bisulfite sequencing before male pronucleus demethylation (demethylation start at PN3 stage, we can use sperm to mimic this) and after demethylation (PN4-5 stages, we have isolated 1000 pronuclei one by one from 1000 PN4-5 stage embryos). We can send you the samples when you are ready. 2. Understand the role of Tet1 in PGC demethylation. As you know, PGC demethylation starts at E9.5 and complete at E13.5. Therefore, we first need to find out what is demethylated in wild-type PGC by comparing the bisulfite result at E9.5 and E13.5. Then, we want to know what is not demethylated after Tet1 KO at E13.5. Therefore, meaningful sample should be wild-type PGC at E9.5 and E13.5 as well as mutant E13.5 PGC. I want to note that at E13.5, male PGC and female PGC can be distinguished. The methylation pattern of imprinted genes and sex chromosomes can be different in male and female PGC. Attached is an inventory that include what Kwonho has sent and what he has collected and has not sent. Received on 8.10.11 #. E9.5 wildtype: 3 tubes (~250, ~250 and ~600 cells) #. E11.5 wildtype: 3 tubes (~700, ~1000, ~1000 cells) #. E13.5 wildtype-male: 2 tubes (~5000 and ~5000 cells) #. E13.5 wildtype-female: 2 tubes (~2000 and ~3000 cells) #. E13.5 mutant-male: 2 tubes (~300 and ~800 cells) #. E13.5 mutant-female: 2 tubes (~1000 and ~800 cells) cDNA library:[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-7-6] RNAseq library:[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-7-11] RNAseq run: HL098 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui_Liu#HL098] HL101 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui_Liu#RNA_libraries_for_Dr._Yi_Zhang_lab] Hiseq111005 ====Human ES differentiation samples==== Project: perform RNA-seq to compare the gene expression during endoderm differentiation of human ES cells. Analyze ES, definitive endoderm, and pancreatic progenitor cells by RNA-seq. ctr/0d, B1/0d, B3/0d, ctr/2d, B1/2d, B3/2d. one gene plays an important role for definitive endoderm differentiation. compare the gene/non-coding RNA expression during the first stage differentiation, in control and knock-down cells. Received on 9.15.11, 1000c/tube #. ctr/0d #. B1/0d #. B3/0d #. ctr/2d #. B1/2d #. B3/2d cDNA library:[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-10-3] RNAseq library:[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-10-12] RNAseq run:HL106 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui_Liu#HL106] HL107 Received on 12.10.11, 1000c/tube (24 tubes) Two ES samples: marked with "H9/45 ES, 11/4/11" (#1) and "H9/50 ES, 11/28" ((#2)) Two DE samples: marked with "H9/41 DE, 10/20" (#3) and "H9/46f DE, 10/31" (#4) Three PP samples: marked with "S3/f, 10/14" (#5) "S3/f P2, 10/14" (#6) "62M, 24+, 10/26" (#7) Two alpha samples: marked with "alpha, 11/17" (#8) and "alpha, 11/11" (#9) Two beta samples: marked with "beta, 11/17" (#10)"beta, 11/11" (#11) One exocrine sample: marked with "Px+, 11/17" (#12) cDNA library: RNAseq library: RNAseq run: ===Dr. Yang Xu lab=== * 6/27/11: # GFP(+), Pancreatic lineage differentiated from hESC, NGN3+ (~50000 cells, purified with Qiagen RNeasy), 20.8ug/ml, use 1ul # GFP(-), Pancreatic lineage differentiated from hESC, NGN3- (~50000 cells, purified with Qiagen RNeasy), 12.7ug/ml, use 1ul cDNA library lab note: [http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/SingleCellExpr/2011-7-5] RNAseq library lab note: [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-7-11] RNAseq run analysis: [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui_Liu#HL098] * 7/7/11: Origin (?) Method (cell sorting --> spin top speed for at least 5min, done by Dae-Hwan) # Negative control (No fluorescence)--- 2 tubes (>200,000 cells each) # RFP positive ------ 1 tube (~12,000 cells) # GFP/RFP double positive ------ 1 tube (~55,000 cells) cDNA library lab note:[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-10-3#cDNA_libraries] RNAseq library lab note: [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-10-11] RNAseq run analysis: [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui_Liu#HL106] * 9/28/11: 3 samples from Dr. Xu lab by Alice, RNA samples from sorted neural stem cells from nestin-rfp knockin hESCs. # Low is rfp low # high rfp high # fetal NSCs are the human fetal cells. cDNA library lab note:[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-10-3#cDNA_libraries] RNAseq library lab note: RNAseq run analysis: ===Dr. Juan Carlos Izpisúa Belmonte lab=== * Athanasia iPS colonies samples in "Belmonte lab" box at -80C * Fibroblast samples: 2 tubes received on 11.10.11 (50k cell/tube; 500k cell/tube) in "collaboration" box at -80C * Samples are used for whole genome sequencing and exome sequencing ==Quick note== MmeI primer digestion [http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-3-18 ] {| {{table}} border=1 | align="center" style="background:#f0f0f0;"|'''50 cells RNAseq''' | align="center" style="background:#f0f0f0;"|'''procedure''' | align="center" style="background:#f0f0f0;"|'''samples''' | align="center" style="background:#f0f0f0;"|'''start''' | align="center" style="background:#f0f0f0;"|'''end''' | align="center" style="background:#f0f0f0;"|'''note''' |- | ~25 cells||RNA or lysate||Sperm vs ES cells||5.19.11||5.20.11|| |- | ||||process, clone||5.21.11||5.24.11||5.25.11 seq result |- | ||||Nextera library||5.23.11||5.23.11||spread out (clone?) |- | ||||Solexa library||5.23.11||5.23.11||amp. Not good |- | ||||||5.26.11||5.26.11||again. Not good |- | ||||||6.1.11||6.2.11||different buffs |- | ||||||6.2.11||6.3.11||another 2ug repeat |- | ||||||6.4.11||||Kapa for NGS |} ==2012== <calendar> name=Rui:LabNotes/Collaborations format=%name/%year-%month-%day date=2012/10/1 view=oneyear </calendar> ==2011== <calendar> name=Rui:LabNotes/Collaborations format=%name/%year-%month-%day date=2011/10/1 view=oneyear </calendar>
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