Below is a list of all experimental records and data. Records typically include a sample ID as well as a link to files for that run. These files are stored on a google drive that will require access in order to download. Some of these files have been compressed to reduce file size and increase the ease of transferring to and from storage. All records here are backed up on the lab drive in their respective project folders as well.

Tip

I have begun to compress these files for long term storage in the cloud and on the lab drive. They can be compressed with the following terminal command (Mac) tar -czf foldername.tar.gz foldername. These can be uncompressed with tar –xf foldername.tar.gz.

It is also noteworthy that you can download from the google drive in R directly using library("googledrive") and drive_download("filename.tar.gz", path = "outputpath/filename.tar.gz", overwrite=TRUE). If no input path is given and you just put "filename.tar.gz" in both fields, it will download to R's current working directory.

M6A G-RAMP

Below is a sortable table for all Nanopore m6A RNA runs conducted in the Lai Lab. These data are also stored on the lab drive in addition to a google drive backup.

Entry	Sample ID (Notebook Reference)	Protocol	Cell Line	IDH Status	Output	Reads	Notes	Date of Run
27	AS76LB4766WT324 (LLT-001p108)	Nanopore RNA Sequencing Protocol	LB4766	WT	Okay	22.69k	Same sample as previous entry, used remaining library amount. 59 pore flow cell.	3/25/24
26	AS56LB4766WT324 (LLT-001p108)	Nanopore RNA Sequencing Protocol	LB4766	WT	Good	110.81k	Same sample as previous entry, but I loaded only 5 μL of eluted library since library was very concentrated. Good results. 90-100 pore flow cell.	3/22/24
25	AS47LB4766WT324 (LLT-001p108)	Nanopore RNA Sequencing Protocol	LB4766	WT	Good	70.31k	Same sample as previous entry, but I loaded only 5 μL of eluted library since library was very concentrated. Good results. 73 pore flow cell.	3/21/24
24	AS32LB4766WT324 (LLT-001p107)	Nanopore RNA Sequencing Protocol	LB4766	WT	Okay	38.19k	Extraction and run with LB4766 sample. mRNA from this sample appeared dilute (21.3 ng/μL), so I used 10 μL mRNA for nanopore library prep, reducing H20 to 8 μL in step 5. Eluted in 15 μL of buffer at the end of the Nanopore protocol. 7 μL of final library sample was loaded with 9 μL / 14 μL LBII and SBII. Flow cell appeared overloaded.	3/20/24
23	AS80LB4424MUT324 (LLT-001p106)	Nanopore RNA Sequencing Protocol	LB4424	Mut	Good	64.19k	Library prep using frozen mRNA extracted from LB4424. Concentration of the mRNA input was low (19 ng/μL), so I increased the input slightly and decreased the water loaded at step 5 in the protocol. Loaded 10 μL of library with 9 μL / 14 μL LBII and SBII. Might have slightly overloaded the flow cell.	3/18/24
22	AW25LB5121MUT324 (LLT-001p105)	Nanopore RNA Sequencing Protocol	LB5121	Mut	Good	82.89k	Left over library run a day later from the previous protocol. Ended up loading ~10 μL of library (remaining) and 9 μL / 14 μL of loading beads and sequencing buffer. Note: Naming for this one was incorrect for the flow cell ID, because I was in a hurry. I left it as is so it matches with the folder in minKNOW on the linux workstation.	3/15/24
21	AS52LB5121MUT324 (LLT-001p105)	Nanopore RNA Sequencing Protocol	LB5121	Mut	Good	84.81k	Run on an IDH-Mut patient sample. Extracted total and mRNA on the same day as the run using the direct mRNA kit and TRIzol. Note: Naming for this one was incorrect for the flow cell ID, because I was in a hurry. I left it as is so it matches with the folder in minKNOW on the linux workstation.	3/13/24
20	AQ14LB4424MUT224 (LLT-001p101)	Nanopore RNA Sequencing Protocol	LB4424	Mut	Poor	4.41k	Reused the same library from the previous day, but on a new Flongle. Flongle was below warranty and the re-used library was suboptimal after freeze/thaw.	2/22/24
19	AQ86LB4424MUT224 (LLT-001p101)	Nanopore RNA Sequencing Protocol	LB4424	Mut	Okay	32.01k	This was on a sub-optimal below warranty Flongle (36 pores available). This run was different because I re-measured the concentration of mRNA after thawing, loading 9 μL of 35 ng/μL starting mRNA. Eluted the final elute volume into 15 μL instead of 21 μL, and loaded 7 μL library (with 9 μL LBII and 14 μL SB). The library prep was good and had good pore occupancy, but the Flongle was a below warranty Flongle.	2/21/24
18	AQ84LB4424MUT224 (LLT-001p100)	Nanopore RNA Sequencing Protocol	LB4424	Mut	Okay	22.44k	Run using left over library from the previous two runs. This was on a sub-optimal below warranty Flongle.	2/20/24
17	AQ23LB4424MUT224 (LLT-001p100)	Nanopore RNA Sequencing Protocol	LB4424	Mut	Okay	23.95k	Run using left over library from the previous run. This was on a sub-optimal below warranty Flongle.	2/17/24
16	AQ12LB4424MUT224 (LLT-001p100)	Nanopore RNA Sequencing Protocol	LB4424	Mut	Okay	39.87k	Run using patient mRNA that had been previously frozen and stored at -80ºC. Eluted into 21 μL twice. Used 7 μL library, 9 μL LBII and 14 μL SB. This was done on a Flongle with 66 pores available, but note that this Flongle had previously reported 71 pores (8/1/23) and 1 pore (1/25/24) respectively. Flongle slightly underloaded, which I found out later after having to pipette mRNA after freezing which showed a lower concentration.	2/16/24
15	AQ73LB5139WT124 (LLT-001p96)	Nanopore RNA Sequencing Protocol	LB5139	WT	Okay	32.23k	Run using left over prepared library from the previous two entries, frozen at -20ºC and thawed twice. The flow cell was below warranty. Pore decay and pore occupancy were optimal for a below warranty flow cell.	1/27/24
14	AQ61LB5139WT124 (LLT-001p96)	Nanopore RNA Sequencing Protocol	LB5139	WT	Okay	45.42k	Run using left over prepared library from the previous entry, frozen at -20ºC and thawed the next day. The flow cell used was one near below warranty (~52 pores available at the start). Pore decay and pore occupancy were optimal.	1/24/24
13	AQ97LB5139WT124 (LLT-001p96)	Nanopore RNA Sequencing Protocol	LB5139	WT	Good	102.68k	First run with patient tissue. Patient was a GBM grade IV. Starting material was a 60 mg piece of tumor that was run through a trizol total RNA extraction protocol, followed by mRNA purification using the direct mRNA kit. RNA was exceptionally pure.	1/23/24
12	AP56HK217W124 (LLT-001p91)	Nanopore RNA Sequencing Protocol	HK217	WT	Okay	44.38k	Used the mRNA extracted from the previous run, so it was a few days old and had been freeze/thawed. I spiked in m6A positive and negative controls (0.5 μL each) and 9 μL of the mRNA extract that was around 225 ng total. Pore decay was a tad faster; I eluted in 13 μL at the end to try to improve throughput from entry 11. No real improvement. Input mRNA should be 330 ng always.	1/11/24
11	AQ43HK217W124 (LLT-001p90)	Nanopore RNA Sequencing Protocol	HK217	WT	Okay	42.19k	This was freshly extracted mRNA, no rRNA cleanup step. Input mRNA was ~25 ng/μL, for about 225 ng total loaded in 9 μL. Pore decay was slow, the Flongle was just underloaded.	1/10/24
10	AQ45U8W1123 (LLT-001p87)	Nanopore RNA Sequencing Protocol	U87	WT	Good	81.02k	This was freshly extracted mRNA, no rRNA cleanup step. Differences in this run: mRNA input was checked for 2.0 or greater ratio in 260/230 and 260/280 regions. mRNA input was the full 9 μL, for around 333 ng of mRNA total. I also turned the pellet fast during ethanol wash, pipetted instead of flicked the tube, and eluted twice. These changes were added to the protocol.	11/09/23
9	FC14U8W723 (LLT-001p71-72)	Nanopore RNA Sequencing Protocol	U87	WT	Good	56k	This was a test run using stored U87 cell RNA that had been purified for mRNA prior to the run. This run generated a decent output.	07/14/23
8	FC31HKW623 (LLT-001p67)	Nanopore RNA Sequencing Protocol	HK217	WT	Okay	-	This was a control run, which mostly contained synthetic RNA oligos containing Gluc/Cluc and m6A modifications. Run on a flongle flow cell. HK217 IDH-WT spiked in as a control.	06/14/23
7	FC92HKW623 (LLT-001p63)	Nanopore RNA Sequencing Protocol	HK217	WT	Poor	-	This was the first attempt at a control run, which mostly contained synthetic RNA oligos containing Gluc/Cluc and m6A modifications. Run on a flongle flow cell. HK217 IDH-WT spiked in as a control.	06/02/23
6	FC04HKW323 (LLT-001p24-25)	Nanopore RNA Sequencing Protocol	HK217	WT	Good	57.41k	This run was a decent run using a Flongle Flow Cell and a gliomasphere cell line.	03/16/23
5	FR56U8W1221	Nanopore RNA Sequencing Protocol	U87	WT	Good	-	This was the vector control U87 re-run by Terry Prins and Sean Pianka. This run yielded a good throughput.	12/20/21
4	FQ15U8W921	Nanopore RNA Sequencing Protocol	U87	WT	Poor	-	This is a vector control U87 sample run by Bryan Kevan and Sean Pianka. This run yielded a very low amount of reads before failing.	09/17/21
3	FO96U8W521	Nanopore RNA Sequencing Protocol	U87	WT	Poor	-	This is a vector control U87 sample run by Bryan Kevan and Sean Pianka. This run did not yield an optimal amount of reads.	05/05/21
2	FM31U8M720	Nanopore RNA Sequencing Protocol	U87	Mut	Good	-	This sample was a U87 sample run by Bryan Kevan and Sean Pianka.	07/15/20
1	FM68U8W720	Nanopore RNA Sequencing Protocol	U87	WT	Poor	-	This is a vector control U87 sample run by Bryan Kevan and Sean Pianka. This run did not yield an optimal amount of reads.	07/14/20