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Status |
Public on Apr 24, 2024 |
Title |
Schwann Cells, NF2-WT, Passage 7, Replicate 2 |
Sample type |
SRA |
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Source name |
Schwannoma
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Organism |
Homo sapiens |
Characteristics |
tissue: Schwannoma cell type: Schwann Cells genotype: NF2-WT
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Extracted molecule |
genomic DNA |
Extraction protocol |
genomic DNA was extracted using the QIAamp DNA Blood Maxi kit (#51192, Qiagen) A total of 140 PCR reactions were performed using 1μg of genomic or plasmid library DNA, Q5 Hot Start HF polymerase (#M0493L, NEB), and primers harboring the Illumina TruSeq adapter sequences. PCR products were purified using DNA Clean and Concentrator TM-100 (#C1016-50, Zymo Research) and MagSi-NGSprep Plus beads (#SL-MDKT-01500, Steinbrenner). Sample concentrations were measured using Qubit HS DNA Assay (#Q32851, Thermo Fisher). Library amplicon size was verified using DNA High Sensitivity Assay on a BioAnalyzer 2100 (Agilent) and then sequenced on a NextSeq (Illumina) by 75bp single-end sequencing and addition of 25% PhiX control v3 (Illumina).
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
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Data processing |
Adapters were trimmed with cutadapt Reads were aligned to a FASTA file containing sequences of all the sgRNAs in the library using bowtie2 Reads per sgRNA were counted using custom software ("count_features") available at https://github.com/aurelioteleman/Teleman-Lab Assembly: N/A Supplementary files format and content: tab-delimited file containing raw read counts for all samples as well as read counts normalized to library size
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Submission date |
Dec 01, 2022 |
Last update date |
Apr 24, 2024 |
Contact name |
Aurelio A Teleman |
Organization name |
German Cancer Research Center (DKFZ)
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Street address |
Im Neuenheimer Feld 580
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City |
Heidelberg |
ZIP/Postal code |
69120 |
Country |
Germany |
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Platform ID |
GPL11154 |
Series (2) |
GSE219136 |
Screen for genes showing synthetic lethality with NF2 in Schwannoma [Other] |
GSE219141 |
Screen for genes showing synthetic lethality with NF2 in Schwannoma |
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Relations |
BioSample |
SAMN31956654 |
SRA |
SRX18443446 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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