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| Status |
Public on Apr 24, 2024 |
| Title |
Schwann Cells, NF2-KO, Passage 7, Replicate 1 |
| 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-KO
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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 |
SAMN31956652 |
| SRA |
SRX18443448 |
| 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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