User:Karmella Haynes/Notebook/PcTF Genomics/2013/06/26: Difference between revisions
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* Step 3, 4 - Add Experiments to Import: added '''6_aln_sorted.bam''' (H3K27me3 ChIP), and '''inputU2OS.bam''' (DNA purified from unenriched chromatin) | * Step 3, 4 - Add Experiments to Import: added '''6_aln_sorted.bam''' (H3K27me3 ChIP), and '''inputU2OS.bam''' (DNA purified from unenriched chromatin) | ||
* Step 5 - Create binding proteins: created "H3K27me3" for 6_aln_sorted. | * Step 5 - Create binding proteins: created "H3K27me3" for 6_aln_sorted. | ||
* Set control inputU2OS as "yes" for "Is control?" | * Step 6 - Assigned H3K27me3 as protein label for 6_aln_sorted; Set control inputU2OS as "yes" for "Is control?"; Set inputU2OS as control for 6_aln_sorted. | ||
* Step 11 - Chose BED files only (wigs take up lots of disk space) | |||
* Step 12 - Deselected "Directionality" | |||
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'''U2OS TRIzol prep'''<br> | '''U2OS TRIzol prep'''<br> | ||
# | # +PcTF, plate 1-A | ||
# | # +PcTF, plate 1-B | ||
# mock, plate 4-A | |||
# mock, plate 4-B | |||
(Should provide more than enough RNA. Discarded other cultures) | |||
* Cells were 100% confluent | |||
* Discarded growth medium | * Discarded growth medium | ||
* Added | * Added 2 mL TRIzol directly to plates | ||
* Incubated at r.t. for ~5 min. | * Incubated at r.t. for ~5 min. | ||
* Collected lysed cells from plate with gentle scraping (pipette tip) | * Collected lysed cells from plate with gentle scraping (pipette tip) | ||
* Transferred | * Transferred 500 μL aliquots to 2.0 mL tubes. Stored at -80°C | ||
** 8x PcTF+ samples | |||
** 8x mock samples | |||
Revision as of 21:14, 27 June 2013
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06/26/13
ChIP seq analysis with Input control Array Star analysis - general instructions
H3K27me3 enrichment in U2OS
U2OS TRIzol prep
(Should provide more than enough RNA. Discarded other cultures)
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