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| Status |
Public on Mar 21, 2024 |
| Title |
Replicate 4, Fraction D |
| Sample type |
SRA |
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| Source name |
LP+Reporter cells (this study)
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| Organism |
Homo sapiens |
| Characteristics |
cell line: LP+Reporter cells (this study)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from each fraction using a Monarch Genomic DNA Purification Kit (NEB #T3010) following the manufacturer's recommended protocol.
Barcode sequences were amplified from gDNA using a two-step protocol: gDNA was first amplified with primers JLSPr141–144 and JLSPr165–168+171+172 using Q5 High-Fidelity DNA Polymerase (NEB #M0491) for 20 cycles with an annealing temperature of 65°C, and then with primers IDT10_i7_NN and IDT10_i5_NN, where NN is replaced with the unique indexing barcode ID, for sample multiplexing (10 cycles, 65°C annealing temperature).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq X Plus |
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| Data processing |
*library strategy: Barcode amplicon sequencing
Reads were cleaned with fastp (v0.23, with default parameters). Barcodes were extracted and counted using a custom script. vBCs were mapped to variants using the results of the PacBio long-read sequencing of the barcoded plasmid library. vBCs failing to match an expected barcode from the PacBio sequencing were error-corrected up to a Hamming distance of 1, if and only if they could be unambiguously mapped to an expected variant.
Assembly: Alignment not performed
Supplementary files format and content: *.extracted_barcodes.counts.parquet: table of read counts for each vBC-rBC pair, including assigned library variant
Supplementary files format and content: barcode_to_variant_map.tsv: table mapping vBC sequences to library variants, as called from long-read plasmid sequencing data
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| Submission date |
Mar 20, 2024 |
| Last update date |
Mar 21, 2024 |
| Contact name |
Barak Alon Cohen |
| E-mail(s) |
[email protected]
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| Organization name |
Washington University School of Medicine
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| Department |
Genetics
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| Street address |
4523 CLAYTON AVE CB #8510
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| City |
SAINT LOUIS |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL34284 |
| Series (1) |
| GSE262060 |
Functional activity scores of a DMS library representing coding single residue substitution variants in the transcription factor CRX measured in an engineered reporter cell line |
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| Relations |
| BioSample |
SAMN40558887 |
| SRA |
SRX24006044 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8156824_CTRA-4D.extracted_barcodes.counts.parquet.gz |
21.1 Mb |
(ftp)(http) |
PARQUET |
SRA Run Selector |
| Raw data are available in SRA |
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