|
| Status |
Public on Apr 01, 2024 |
| Title |
untreated 4304 donor rep3 |
| Sample type |
SRA |
| |
|
| Source name |
blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
cell type: Washed day 10 erythroid progenitors
treatment: unedited
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Erythroid progenitors were snap frozen and total RNA was extracted.
Sequencing libraries were generated using an Illumina TruSeq Stranded mRNA sample prep kit and sequenced on a NovaSeq V1.5 (both Illumina, Inc.) as paired-end 2x150bp reads by SeqMatic, LLC (San Francisco, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
KW106-16
TruSeq Stranded Total RNA prep
Expression_Norm_gene (6 of the 24 samples were used for variant calling: KW-100-13, KW-100-21, KW-100-29, KW-100-5, KW-106-13, KW-106-5)
|
| Data processing |
CLC Genomics Workbench v 11.0.1
RNAseq reads were aligned to with STAR (v2.7.3a). Read counts for exons were computed with HTseq count using parameters outlined in the Supplemental Methods. Exon/intron counts were normalized by length such that total expression of the HBB gene (sum of wt and edited exon/intron expression) is 1 - analogous to standard TPM normalization for full length transcripts but applied to individual exons/introns.
Assembly: hg38
Supplementary files format and content: txt file w/ counts data
|
| |
|
| Submission date |
Apr 07, 2023 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Kristen Seim |
| E-mail(s) |
kristen.seim@gmail.com
|
| Organization name |
GraphiteBio
|
| Street address |
201 Haskins Way
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE229212 |
Development of a ß-Globin Gene Replacement Strategy as a Therapeutic Approach for ß-Hemoglobinopathies |
|
| Relations |
| BioSample |
SAMN34115864 |
| SRA |
SRX19907185 |
