| Chemicals, Peptides, and Recombinant Proteins |
| Micrococcal nuclease |
Sigma |
Cat # N3755 |
| RNase T1 |
Life Technologies |
Cat # AM2280 |
| IgG Sepharose Fast Flow |
Fisher Scientific |
Cat # 45000173 |
| AcTEV protease |
Life Technologies |
Cat # 12575023 |
| Calmodulin Affinity Resin |
Agilent |
Cat # 214303 |
| Debranching enzyme (DBE) |
A gift from Dr. Schwer |
N/A |
| Branched oligo (bRNA) |
A gift from Dr. Damha |
N/A |
| SuperScript III Reverse Transcriptase |
ThermoFisher |
Cat # 18080-044 |
| T4 RNL2Tr.K227Q |
NEB |
Cat # M0351L |
| CircLigase |
Illumina, Inc |
Cat # CL4115K |
| 2x KAPA HIFi Kit |
Kapa Biosystems |
Cat # KK2611 |
| GoTaq Green |
Promega |
Cat # M7112 |
| SuperScript III One-Step RT-PCR System with Platinum Taq High Fidelity |
Invitrogen |
Cat # 12574-035 |
| Deposited Data |
| Spliceosome profiling data |
This study |
PRJNA437439 |
| RNA sequencing data |
Marguerat et al., (2012) |
EMBL-EBI: ERR135906, ERR135907 and ERR135910 |
| Sequence conservation scores four-way MULTIZ alignment of the S. pombe, S. octosporus, S. cryophilus, and S. japonicus
|
Rhind et al., (2011) |
ftp://ftp.broadinstitute.org/pub/annotation/fungi/schizosaccharomyces/supplementary_downloads/SP.cons.wig.gz |
| Experimental Models: Organisms/Strains |
|
S. pombe: Wild Type (WT) cells (ura4-D18 leu1-32 h-) |
This study |
N/A |
|
S. pombe: upf1Δ cells (upf1Δ, ura4-D18 leu1-32 h-) |
This study |
N/A |
|
S. pombe: Triply-tagged (TT) cells (Cdc5-GFP, Lea1-Protein A, Snu114-CBP, ura4-D18 leu1-32 h-) |
Chen et al., (2014) |
N/A |
|
S. pombe: TT dbr1Δ (dbr1Δ, Cdc5-GFP, Lea1-Protein A, Snu114-CBP, ura4-D18 leu1-32 h-) |
This study |
N/A |
| Oligonucleotides |
| Primer: adh4 Forward: 5′-GTGACCATTCATATTGCTTGG-3′ |
This study |
N/A |
| Primer: adh4 Reverse: 5′-TTGGCGGCTTCAGCAAG-3′ |
This study |
N/A |
| Primer: SPSNORNA.02-0.6 Forward: 5′-GCCAGTATACGGCGTTGTTAG-3′ |
This study |
N/A |
| Primer: SPSNORNA.02-0.6 Reverse: 5′-GTTGATCGTAAATCCCTTCTGTTC -3′ |
This study |
N/A |
| Primer: lea1 Forward: 5′-AGG TAC CCT CAT TCA TCA G -3 |
This study |
N/A |
| Primer: lea1 Reverse: 5′-CGG TTA TTT CCA CAC AAA AGC -3′ |
This study |
N/A |
| Primer: SPNCRNA.445 Forward: 5′-GTT GTG CTG GTG ATA TCG -3′ |
This study |
N/A |
| Primer: SPNCRNA.445 Reverse: 5′-CTT GGT ATC AGG TTG TCT TC -3′ |
This study |
N/A |
| Primer: prp10 Forward: 5′-GCT TCG TGC TGA AAG AG-3′ |
This study |
N/A |
| Primer: prp10 Reverse: 5′-TCA TAT TGA CGC ACT AAA CG-3′ |
This study |
N/A |
| Primer: adh4 primer extension: 5′-GGCTTTCGAAGAGGTTGATTGATG-3′ |
This study |
N/A |
| Software and Algorithms |
| Cutadapt V1.71 |
Martin (2011) |
https://github.com/marcelm/cutadapt/ |
| Fastx Toolkit V0.0.14 |
http://hannonlab.cshl.edu/fastx_toolkit/ |
https://github.com/agordon/fastx_toolkit |
| Bowtie2 V2-2.1.0 |
Langmead et al. (2012) |
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Branchpoint (BP) Identification by Random Forest Algorithm |
This Study |
https://github.com/Jill-Moore/SPombe-Splicing/ |
| Branchpoint (BP) Identification Branch ALigner (BAL) |
This Study |
https://github.com/hakanozadam/bal |
| Other |
| Ball Mill |
Retsch |
PM 100 |
