|
| Status |
Public on Apr 07, 2020 |
| Title |
RIP using strain containing no tags |
| Sample type |
SRA |
| |
|
| Source name |
log. growing cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
growth stage: log. growing cells
genotype: wild type cells
rip antibody: GFP antibodies (Abcam, ab290, Lot#: GR306215-1)
|
| Growth protocol |
Standard conditions were used for logarithmically growing cultures in rich media (YEA). Cultures were grown at 32C overnight.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde at room temperature for 20 minutes. Cells were lysed and were sonicated using bioruptor. Immunoprecipitations were performed using GFP antibodies (ab290). Reverse crosslinking was performed overnight at 65˚C and protein was degraded using proteinase K. RNAase free DNAase I (Thermo Fisher, am2222) was used to degrade DNA fragments and RNA was purified using phenol-chloroform and ethanol precipitation.
NEB Ultra Directional RNA Library Prep kit (NEB, E7420S) was used according to manufacturer's recommendation.
Libraries were analyzed using an Agilent 4200 TapeStation system (Agilent) and sequenced on the Illumina NextSeq 500 platform.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Untagged-GFP RIPseq
PIR2_RIP_untagged_subtracted_forward.bedgraph
PIR2_RIP_untagged_subtracted_reverse.bedgraph
|
| Data processing |
Alignment was done using Tophat.
Reads Per Kilobase of transcript, per Million mapped reads (RPKM) values were obtained using Deeptools suite.
Alignments were strand separated using Samtools
RPKM Normalized Untagged RIPseq was subtracted from RPKM normalized Pir2-GFP RIPseq using deeptools-bamCompare.
Genome_build: asm294v2.28
Supplementary_files_format_and_content: bedgraph
|
| |
|
| Submission date |
Jul 31, 2019 |
| Last update date |
Apr 07, 2020 |
| Contact name |
Shiv Grewal |
| Phone |
2407607553
|
| Organization name |
NCI
|
| Department |
LBMB
|
| Lab |
Shiv Grewal
|
| Street address |
NCI bldg 37 Rm 6068 9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL20584 |
| Series (2) |
| GSE135158 |
Cryptic introns in lncRNAs recruit conserved Pir2/ARS2 protein to promote gene repression [RIP-seq] |
| GSE135161 |
Cryptic introns in lncRNAs recruit conserved Pir2/ARS2 protein to promote gene repression |
|
| Relations |
| BioSample |
SAMN12404870 |
| SRA |
SRX6619814 |
