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| Status |
Public on Apr 02, 2015 |
| Title |
501_shSCR1_rep2 |
| Sample type |
SRA |
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| Source name |
501Mel
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| Organism |
Homo sapiens |
| Characteristics |
cell line: 501Mel
cell type: melanoma
knockdown: shSCR1
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation from 501M or Hermes3A cells was performed according to standard procedure (Qiagen kit). 1,5 μg of RNA was reverse transcribed using a mix 1/1 of SuperScript II RNase H-reverse transcriptase (Invitrogen) and AMV retrotranscriptase (Roche) with 500 ng of oligodT22 primer, hexanucleotides or specific primers according to the manufacter’s instructions
Total RNA-seq libraries were prepared following the Illumina protocol with some modifications. Briefly, 2 µg of total RNA was hybridized with rRNA sequence-specific 5’biotin labeled oligonucleotide probes to selectively deplete ribosomal RNA. The rRNA/5’biotin labeled probe was removed from the sample with streptavidin-coated magnetic beads. (Ribominus Eukaryote kit for RNA-seq, #A10837-08, Invitrogen Corporation). The rRNA depleted RNAs were then fragmented using divalent cations at 95°C for 5 minutes and used to generate a reverse transcribed cDNA library. 100 ng of each DNA library was then denatured at 98°C for 2 minutes, incubated at 68°C for 5 hours and then incubated in the presence Duplex-Specific thermostable Nuclease enzyme (DSN, #EA001, Evrogen) for DSN normalization following the Illumina protocol. DSN treated libraries were purified using Agencourt AMPure XP beads, enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 6 cycles; 5 min at 72°C) and purified again using Agencourt AMPure XP beads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina Casava v1.8 software was used for basecalling.
Sequence reads were mapped onto the hg19 assembly of the human human using Tophat v1.4.1 and the bowtie v0.12.7 aligner.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file corresponding to abundance measurements (raw read counts for each ensembl gene id) for each sample
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| Submission date |
Oct 01, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Patrick Laurette |
| Organization name |
IGBMC
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| Street address |
1 Rue Laurent Fries
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| City |
Illkirch |
| ZIP/Postal code |
67404 |
| Country |
France |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE61966 |
BRG1 recruitment by transcription factors MITF and SOX10 defines a specific configuration of regulatory elements in the melanocyte lineage (RNA-seq) |
| GSE61967 |
BRG1 recruitment by transcription factors MITF and SOX10 defines a specific configuration of regulatory elements in the melanocyte lineage |
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| Relations |
| BioSample |
SAMN03085834 |
| SRA |
SRX718675 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1517759_501_readcount_shSCR1_rep2.txt.gz |
174.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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