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| Status |
Public on Aug 01, 2023 |
| Title |
GFP Neg, day 3, replicate 1 |
| Sample type |
SRA |
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| Source name |
HCT116
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
genotype: reporter DNA integrated at H1 landing pad
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| Growth protocol |
HCT116 cells were maintained following ATCC recommended guidelines
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using PureLink Genomic DNA Mini Kit (Invitrogen #182001) following manufacturer's protocol
NGS library was prepared following Illumina's Metagenomic Sequencing Library Preparation protocol to add sequencing indexes by 2-step PCR
Amplicon sequencing to determine the relative abundace of barcoded DNA
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina), and then evaluated for quality control (QC) with FastQC.
Fastq files were then converted to Fasta files using the FASTX-Toolkit. Fasta files were trimmed to remove shared linker sequence and to retain regions in each read with high quality (Phred Score > 25.75 as determined by FastQC).
To map each NGS read to the library, we created a local blast database containing SHIELD library sequences, and used the BLAST+ 2.7.1. module to perform alignment analysis of NGS data against library database.
For post-alignment data processing, we first removed duplicates (i.e., one read being mapped to multiple library sequences) and kept only one alignment with the highest bitscore (lowest e-vaule) for each read. In addition, we removed alignments with more than 3 mismatches, or more than 3 gaps, or with a total mapped length less than the maximum possible minus 10 nucleotides.
Assembly: n.a.
Supplementary files format and content: Tab-delimited text file including raw counts for each DNA element in the library
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| Submission date |
Jun 29, 2023 |
| Last update date |
Aug 01, 2023 |
| Contact name |
Meng Zhang |
| Organization name |
Stanford
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| Street address |
443 Via Ortega
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL15520 |
| Series (1) |
| GSE236198 |
SHIELD: A platform for high-throughput screening of barrier DNA elements in human cells |
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| Relations |
| BioSample |
SAMN36083359 |
| SRA |
SRX20835613 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7519624_NGS4_D3_P1_Neg_R1_BlastCounts_MZ.xlsx |
4.9 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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