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Status |
Public on May 01, 2024 |
Title |
Bottom1 |
Sample type |
SRA |
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Source name |
HFF-1
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Organism |
Homo sapiens |
Characteristics |
cell line: HFF-1 cell type: fibroblasts treatment: Collected from the bottom surface of transwell after the first round of selection
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Treatment protocol |
Cells were transduced with the Human Genome-Scale CRISPR Knock-Out (GeCKO) lentiviral pooled library (GeCKO v2, library A, cat. 1000000048, Addgene), and cultured either in standard flasks or in transwell devices.
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Growth protocol |
HFF were maintained in Dulbecco's modified Eagle Medium (DMEM, cat. 11965, ThermoScientific) supplemented with 15% fetal bovine serum (FBS, ThermoScientific) at 37°C and 5% CO2. Cells were maintained on culture-ware (including transwells) coated with Matrigel growth factor reduced (MGFR, 50 μg/mL overnight at 4°C and 1 h at 37°C, cat. 354230, Corning) and passaged by 0.25% trypsin digestion (ThermoScientific) before reaching confluency.
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Extracted molecule |
genomic DNA |
Extraction protocol |
Genomic DNA was extracted using Quick-gDNA MidiPrep (Zymo Research) following manufacturer's instructions Genomic DNA amplification for Next Generation Sequencing analysis was performed according to Joung et al. (10.1038/nprot.2017.016) Library preparation for Next Generation Sequencing analysis was performed according to Joung et al. (10.1038/nprot.2017.016)
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
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Data processing |
Illumina binary base call (BCL) files were converted into fastq file format by Illumina bcl2fastq software (v. 2.17). Paired reads were merged using Pear (v. 0.9.11), and trimmed using cutadapt (v. 2.8). The trimmed reads were mapped to the human GeCKOv2 library by Bowtie (v. 1.2.3). The sgRNA count matrix was obtained from Bowtie output sam files. Data from each sample were merged into a single table of unfiltered counts with R software (v. 4.2.2). Assembly: Human Genome-Scale CRISPR Knock-Out (GeCKO) lentiviral pooled library (GeCKO v2, library A, cat. 1000000048, Addgene) Supplementary files format and content: Tab delimited file containing the unfiltered counts from Bowtie alignment
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Submission date |
Apr 30, 2024 |
Last update date |
May 01, 2024 |
Contact name |
Camilla Luni |
Organization name |
University of Bologna
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Department |
DICAM
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Street address |
Via Terracini 28
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City |
Bologna |
ZIP/Postal code |
40131 |
Country |
Italy |
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Platform ID |
GPL11154 |
Series (1) |
GSE266226 |
Functional CRISPR-Cas9 knockout screening of the genetic determinants of human fibroblast migration propensity |
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Relations |
BioSample |
SAMN41144454 |
SRA |
SRX24416975 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
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