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| Status |
Public on Apr 24, 2015 |
| Title |
L5p_01 Wild Type |
| Sample type |
SRA |
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| Source name |
yeast cells
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| Organism |
Saccharomyces cerevisiae BY4741 |
| Characteristics |
strain: BY4741
genotype: Wild Type (BY4741 can1_delta)
internal strain reference: LMA1057
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the hot acid phenol protocol (2). Poly(A)+-RNA were obtained by two successive rounds of purification using oligo (dT)25 magnetic beads (New England Biolabs) following the manufacturer's protocol. RNAs were incubated with TAP (Tobacco Acid Pyrophosphatase) and biotynilated. After fragmentation the 5'-end RNAs were purified using strepavidin magnetic beads
RNA libraries were prepared for sequencing using standard Illumina protocols with only a first step to add a specific tag (NNNNCGCGCGNN or NNNNCGCCGGNN) at the 5'-end of each sequence to eliminates further contamination
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 1
5'-end of RNAs
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| Data processing |
Duplicated reads were first eliminated from the sequences. Then tagged reads were extracted from the unique reads searching the specific 5'-end tag (NNCGCGCGNN or NNCGCCGGNN)
After removal of the tag, the resultant reads were aligned the reference genomes using bowtie2
for 5'end samples, only 5' end extremity of each mapped read was conserved and reported in wig files. For full RNA sample, whole reads were used in wig files
for samples 1 to 24, reads count were normalized using the median reads count of the -50 to -10 nucleotides zone before each annotated ORF as reference value
for samples 25 to 40, reads count were normalized using the total S. pombe mapped read count as reference value
bed files correspond to the application of a peak calling procedure on 5'end samples. We followed the method described by Neil et al (2009). We choose as parameters a distance of 150 nucleotide for the maximal distcane between consecutive TSS and a minimum reads count of 4 in at least one of the samples involved in the procedure
the resultant clusters were associated to annotated features using annotation available on SGD. We used ORFs, tRNAs, snRNAs, snoRNAs, rRNAs, ncRNAs, CUTs, SUTs and XUTs
false-positive clusters were filtered out using two parameters; a proportion of TSSs mapped on a purine preceded by a pyrimidine under 80% and a log2(upf1∆rrp6∆-TAP/upf1∆rrp6∆-No-TAP) below 0.55
Genome_build: S. cerevisiae S88C R64-1-1; S. pombe ASM294 v2.19
Supplementary_files_format_and_content: wig: values correspond to the normalized reads count. Negative values correspond to the reads on reverse strand
Supplementary_files_format_and_content: wig: samples L5p_11.XXX correspond to the sum of L5p_01.XXX, L5p_03.XXX and L5p_04.XXX
Supplementary_files_format_and_content: wig: samples L5p_12.XXX correspond to the sum of L5p_02.XXX, L5p_05.XXX and L5p_06.XXX
Supplementary_files_format_and_content: wig: samples L5p_13.XXX correspond to the sum of L5p_07.XXX, and L5p_08.XXX
Supplementary_files_format_and_content: wig: samples L5p_14.XXX correspond to the sum of L5p_09.XXX, and L5p_10.XXX
Supplementary_files_format_and_content: wig: samples LT_03.XXX correspond to the sum of LT_01.XXX, and LT_02.XXX
Supplementary_files_format_and_content: bed: values correspond to the normalized reads count within the cluster in each sample used to generate clusters
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| Submission date |
Dec 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Alain Jacquier |
| E-mail(s) |
alain.jacquier@pasteur.fr
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| Phone |
33-1-4061 3205
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| Organization name |
Institut Pasteur
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| Department |
Génomes & génétique
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| Lab |
Génétique des Interactions macromoléculaires
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| Street address |
25-28 rue du docteur roux
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| City |
Paris cedex 15 |
| ZIP/Postal code |
75724 |
| Country |
France |
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| Platform ID |
GPL18330 |
| Series (1) |
| GSE64139 |
Quality control of transcription start site selection by Nonsense-Mediated-mRNA Decay |
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| Relations |
| BioSample |
SAMN03264411 |
| SRA |
SRX807817 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1565066_L5p_01.WT.wig.gz |
1.4 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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