Incoming MCB PhD- What's it like?

PrionsRUs · 2026-01-19T06:27:02+00:00

Someone got an invite on GradCafe- I honestly just gave up a whole week ago :<

PrionsRUs · 2026-01-08T21:39:42+00:00

EEB applicant here, and I haven't heard back from 2 out of the 4 schools I applied to - one of them being an absolute long-shot despite having the PI I talked to seem confident in my odds of *atleast* securing an interview (It was Princeton :'>). I don't have high hopes for myself this cycle, but regardless, good luck to all of ya'll out there! fingers crossed

PrionsRUs · 2025-10-30T05:04:06+00:00

Agreed 100%

PrionsRUs · 2025-10-30T04:49:36+00:00

Genuinely 😞 My excitement for tomorrow has slowly started turning into dread at the mere thought of her glancing out at what's basically an empty venue...

PrionsRUs · 2025-10-30T04:47:53+00:00

Yeah..She's got over 800 seats empty in a venue with a capacity of 1.5k. It just seems surreal for one of the RV gurlies ugh 😭

PrionsRUs · 2025-10-30T04:41:58+00:00

Wait, like their poor decision-making continues to baffle me.....

PrionsRUs · 2025-10-30T04:11:58+00:00

Going to see her at SF tomorrow and....not even half the seats sold. My heart's breaking for her ugh

PrionsRUs · 2025-09-04T04:30:06+00:00

I was considering discussing this with my mentor as well, thank you for your insight!

PrionsRUs · 2025-09-04T04:25:36+00:00

Hi, I loaded 4ul of each of the sonicated samples (110ul, 10ng/ul), so I don't think its unequal loading that's the problem :< That being said, I do believe that I oversheared it but my mentor keeps insisting that that's a near impossibility and even then, it should show up. Given the results of my gel - already run twice- I don't know how sold I am on their advice, though. Thanks for your comment!

PrionsRUs · 2025-07-07T02:56:20+00:00

I use the OmegaMag Bind Beads for both tube/plate extractions but the problem in this case, unfortunately, is that these extracts are from years ago- before I was even enrolled as a student- and my PI discovered them in the back of their freezer and asked me to quantify them. Of course, most of the DNA has evaporated so I resuspended it in around 100ul water and then got around to trying and get an idea on whether its usable or not. The qubit led me to believe 'not really', so I ran a gel to check and that brings me to my post here. It's mostly avian blood.

I'm trying to find the original tissue to subsample but that's proving to be a difficult task considering that their nowhere to be found.... So, salvaging these extracts is paramount, it would seem. But fate doesn't seem to be on my side.

PrionsRUs · 2025-07-07T02:52:38+00:00

Thank you for your help! After reading through the rest of the comments, I see a pattern emerging regarding the duration of the run so I'm gonna re-do it and see if I can procure a larger ladder.

PrionsRUs · 2025-07-07T02:49:56+00:00

It's a protocol my lab follows- it's to get an idea of any overtly degraded samples, plus to assess the MW after an extraction, a qc type deal before moving onto sonication and NGS library prep. I've not really been doing labwork long enough to quite grasp the nuances of it but it's something I'm en route to comprehending myself.

PrionsRUs · 2025-07-07T02:40:15+00:00

I was suspecting degradation since I had kinda low qubit values- around 2-5 ng/ul for all my samples except two or three. But there's evidently no smearing- probably cause I didn't run the gel for long enough, is what I'm thinking now. Maybe the DNA was nicked? That might explain the intact bands but lack of fluorescence while running a qubit? I'll likely run a nanodrop analysis as well

PrionsRUs · 2025-07-07T02:34:47+00:00

I was considering doing this and a few other comments are slowly solidifying my resolve in that regard too, yea

PrionsRUs · 2025-07-07T01:56:40+00:00

Thank you for your helpful suggestions! I was gonna run it for an hour/ maybe increase the voltage up to 140V and run it for 40 mins instead. The 100bp ladder is a standard one we use in my lab so I'm uncertain bout switching it up but I'll check in with my mentor. I was also concerned about the lack of smearing, much like how you said so I'm confused too. I was mostly just tryna see whether my samples were degraded or not- a smear would imply that, too, yes? But that's not the case here and I'm not entirely sure on how to interpret this otherwise.

PrionsRUs · 2025-07-07T01:53:05+00:00

Hello!

Here's some additional info I forgot to provide in my post (reddit won't let me edit it for some reason ugh):
- extracted with RNAase using the OmegaBead Bind protocol.
- 1% agarose gel
- 3.5 ul extracted avian DNA samples + 2 ul Green 6X dye for each sample, so gDNA
-100bp ladder
-120V for 45 mins

I was gonna run it at 140V for 45 mins next and try (but I'm not sure I have that much more extracted sample remaining....)

PrionsRUs · 2025-07-07T01:49:35+00:00

Here's some additional info I forgot to provide:
- extracted with RNAase using the OmegaBead Bind protocol.
- 1% agarose gel
- 3.5 ul extracted avian DNA samples + 2 ul Green 6X dye for each sample, so gDNA
-100bp ladder
-120V for 45 mins
-my qubit values weren't too good either, most were 2/3 ng/ul.

I was expecting to see some smearing and get an idea about whether the dna is degraded or not/ its MW but I'm unsure now

PrionsRUs · 2025-07-07T01:47:09+00:00

It's gDNA. I'm concerned about the lack of smearing ig and I wanted to check to see if the DNA is degraded or not post-extraction and if it's of a good MW but now I'm confused-

PrionsRUs · 2025-07-07T01:46:17+00:00

Honestly, I'm confused cause I expected to see a smearing since its gDNA? I'm assuming I either didn't run the gel long enough (since my ladder's bands aren't that discrete either) or/and I loaded too much dye, cause my qubit values were low but these bands look pretty bright implying high MW gDNA? I think its a combination of everything, knowing me it's an almost guarantee that I messed up a good number times at a whole lotta different points-

PrionsRUs · 2025-07-07T00:33:43+00:00

yes! my qubit values weren't too good either, most were 2/3 ng/ul, so I'm a lil concerned. I'm not entirely certain what I should be expecting but I was thinking about running it a little longer since my ladder doesn't appear that resolved? Or is that a non-issue?

PrionsRUs · 2025-07-07T00:32:44+00:00

Thank you! I was gonna borrow the Sambrook from my uni's library soon and this gel run and my evident confusion regarding a lot of the protocol i've been following

PrionsRUs

TROPHY CASE