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| Status |
Public on Apr 09, 2024 |
| Title |
secreted round 1 rep A |
| Sample type |
SRA |
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| Source name |
HFF
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| Organism |
Homo sapiens |
| Characteristics |
experiment type: VECOS library screen
time: 10 dpi
cell line: HFF
selection round: 1
replicate: A
targeted gene: NA
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from cells and virus pellets was extracted using a published protocol (Chen et al. 2015, Cell). The viral and cell pellets resuspended in 300 µl and 6 ml of NK buffer, respectively, and DNA extraction was continued normally with volumes adjusted to the 300 µl start, and GlycoBlue™ (Thermo-Fisher, catalog number AM9516) was added at the stage of DNA precipitation.
the region of interest (sgRNA casette or targeted genomic locus) was PCR amplified with addition of illumina adaptors, followed by SPRI bead size selection and purification of the product.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Secreted_round1_repA
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| Data processing |
for sgRNA libraries, MAGeCK v0.5.6 was used to count sgRNA from FASTQ files
for genomic target loci, sequences were aligned to the human genome using STAR v2.5.3a 42 with the following flags: scoreDelBase 0, scoreDelOpen 0, scoreInsOpen 0, scoreInsBase 0, alignIntronMin 300, alignIntronMax 299. The indel rate was calculated as the fraction of reads containing insertions or deletions based on the CIGAR sequence.
Assembly: hg19
Supplementary files format and content: sgRNA_counts.csv is a coma separated file where each line contains an sgRNA name, the gene it targets and the read counts in each of the samples in the paper
Supplementary files format and content: indel_counts.tsv is a tab separated file listing the number of reads containing indels (Indel.reads) and the number of reads without mutations (WT.reads), in each sample. Samples are defined by targeted gene and by time point (tp)
Library strategy: amplicon sequencing
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| Submission date |
Nov 01, 2023 |
| Last update date |
Apr 09, 2024 |
| Contact name |
Noam Stern-Ginossar |
| E-mail(s) |
noam.stern-ginossar@weizmann.ac.il
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| Organization name |
Weizmann Institute
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| Department |
Molecular Genetics
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| Lab |
Noam Stern-Ginossar
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| Street address |
234 herzel
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| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE246735 |
A virally encoded high resolution screen of cytomegalovirus host dependencies |
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| Relations |
| BioSample |
SAMN38058932 |
| SRA |
SRX22326899 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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