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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 23, 2022 |
| Title |
rod photoreceptors, cntl_2 |
| Sample type |
SRA |
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| Source name |
flow-sorted rod photoreceptors
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| Organism |
Mus musculus |
| Characteristics |
cell type: rod photoreceptors
plasmid: control
genotype: control
age: postnatal day 10
replicate: 2
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| Treatment protocol |
EGFP positive rods electroporated with control and Jun shRNA constructs were flow-sorted at P10 as previously described (Kim, Yang et al. 2016).
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| Growth protocol |
shRNA-mediated knockdown of mouse Jun was performed with shRNA-expressing vector (TRC Clone ID TRCN0000042695, MilliporeSigma, Burlington, MA, USA) and control pLKO.1-Scrambled vector (Addgene, Watertown, MA, USA). Nrlp-EGFP vector was adopted from (Kautzmann, Kim et al. 2011). Neonatal mice at P0 were used for in vivo electroporation as previously described (Matsuda and Cepko 2004) with shRNA vectors (2.5 μg/μl, 0.4 μl) and the Nrlp-EGFP vector (1.5 μg/μl, 0.4 μl).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Full length cDNA were generated from purified cells using SMART-seq v4 Ultra Low Input RNA Kit (Takara, Kusatsu, Shiga, Japan). Library generation from cDNA were prepared using Nextera XT DNA Library Kit (Illumina, San Diego, CA, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
postnatal day 10 flow-sorted rod photoreceptors electroporated with control plasmid replicate 2
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| Data processing |
Illumina adapter, polyA, and polyT sequence trimming was performed with Trimmomatic v0.39. Transcript level quantitation was performed using Kallisto v0.44.0 (Bray, Pimentel et al. 2016) employing a merged transcript cDNA and ncRNA FASTA file downloaded from Ensembl v94 (http://oct2018.archive.ensembl.org/index.html).
Gene level quantification performed in R (https://www.r-project.org/) was generated by summarization of the transcript level quantitation using tximport v1.14.0 (Soneson, Love et al. 2015) with the option “countFromAbundance=lengthScaledTPM”.
The gene level count values were TMM normalized in edgeR v3.28.1 package (Robinson, McCarthy et al. 2010).
Genome_build: Ensembl v94
Supplementary_files_format_and_content: Gene_counts.tsv, Gene_normalized-CPM.tsv, Transcript_counts.tsv
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| Submission date |
Feb 24, 2022 |
| Last update date |
Sep 23, 2022 |
| Contact name |
Matthew J Brooks |
| E-mail(s) |
brooksma@nei.nih.gov
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| Phone |
301-443-4906
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| Organization name |
NIH
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| Department |
NEI
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| Lab |
NNRL
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| Street address |
6 Center Dr Bldg 6, Rm 303
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE197384 |
Developmental genome-wide occupancy analysis of bZIP transcription factor NRL uncovers the role of c-Jun in early differentiation of rod photoreceptors in the mammalian retina [RNA-seq] |
| GSE197421 |
Developmental genome-wide occupancy analysis of bZIP transcription factor NRL uncovers the role of c-Jun in early differentiation of rod photoreceptors in the mammalian retina |
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| Relations |
| BioSample |
SAMN26231629 |
| SRA |
SRX14277304 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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